# Patent

## Title
Human analogs of murine deubiquitinating proteases

## Abstract

The present invention is directed to human analogs of murine hematopoetic-specific, cytokine-inducible deubiquinating proteases (“DUBs”) clustered on chromosomes 4 and 8 and their respective regulatory regions. The nucleotides or proteins encoded thereby my be used in assays to identify inhibitors of human DUBs.

## Background
BACKGROUND OF THE INVENTION
The role of ubiquitin in protein degradation was discovered and the main enzymatic reactions of this system elucidated in biochemical studies in a cell-free system from reticulocytes. In this system, proteins are targeted for degradation by covalent ligation to ubiquitin, a 76-amino-acid-residue protein. Briefly, ubiquitin-protein ligation requires the sequential action of three enzymes. The C-terminal Gly residue of ubiquitin is activated in an ATP-requiring step by a specific activating enzyme, E1 (Step 1). This step consists of an intermediate formation of ubiquitin adenylate, with the release of PPi, followed by the binding of ubiquitin to a Cys residue of E1 in a thiolester linkage, with the release of AMP. Activated ubiquitin is next transferred to an active site Cys residue of a ubiquitin-carrier protein, E2 (Step 2). In the third step catalyzed by a ubiquitin-protein ligase or E3 enzyme, ubiquitin is linked by its C-terminus in an amide isopeptide linkage to an -amino group of the substrate protein's Lys residues (Step 3).
Proteins ligated to polyubiquitin chains are usually degraded by the 26S proteasome complex that requires ATP hydrolysis for its action. The 26S proteasome is formed by an ATP-dependent assembly of a 20S proteasome, a complex that contains the protease catalytic sites, with 19S “cap” or regulatory complexes. The 19S complexes contain several ATPase subunits and other subunits that are presumably involved in the specific action of the 26S proteasome on ubiquitinylated proteins. The roles of ATP in the assembly of the 26S proteasome complex and in its proteolytic action are not understood. The action of the 26S proteasome presumably generates several types of products: free peptides, short peptides still linked to ubiquitin via their Lys residues, and polyubiquitin chains (Step 4). The latter two products are converted to free and reusable ubiquitin by the action of ubiquitin-C-terminal hydrolases or isopeptidases (Steps 5 and 6). Some isopeptidases may also disassemble certain ubiquitin-protein conjugates (Step 7) and thus prevent their proteolysis by the 26S proteasome. The latter type of isopeptidase action may have a correction function to salvage incorrectly ubiquitinylated proteins or may have a regulatory role. Short peptides formed by the above processes can be further degraded to free amino acids by cytosolic peptidases (Step 8).
Ubiquitin-mediated degradation of protein is involved in various biological processes. The selective and programmed degradation of cell-cycle regulatory proteins, such as cyclins, inhibitors of cyclin-dependent kinases, and anaphase inhibitors are essential events in cell-cycle progression. Cell growth and proliferation are further controlled by ubiquitin-mediated degradation of tumor suppressors, protooncogenes, and components of signal transduction systems. The rapid degradation of numerous transcriptional regulators is involved in a variety of signal transduction processes and responses to environmental cues. The ubiquitin system is clearly involved in endocytosis and down-regulation of receptors and transporters, as well as in the degradation of resident or abnormal proteins in the endoplasmic reticulum. There are strong indications for roles of the ubiquitin system in development and apoptosis, although the target proteins involved in these cases have not been identified. Dysfunction in several ubiquitin-mediated processes causes pathological conditions, including malignant transformation.
Our knowledge of different signals in proteins that mark them for ubiquitinylation is also limited. Recent reports indicate that many proteins are targeted for degradation by phosphorylation. It was observed previously that many rapidly degraded proteins contain PEST elements, regions enriched in Pro, Glu, Ser, and Thr residues. More recently, it was pointed out that PEST elements are rich in S/TP sequences, which are minimum consensus phosphorylation sites for Cdks and some other protein kinases. Indeed, it now appears that in several (though certainly not all) instances, PEST elements contain phosphorylation sites necessary for degradation. Thus multiple phosphorylations within PEST elements are required for the ubiquitinylation and degradation of the yeast G1 cyclins Cln3 and Cln2, as well as the Gcn4 transcriptional activator. Other proteins, such as the mammalian G1 regulators cyclin E and cyclin D1, are targeted for ubiquitinylation by phosphorylation at specific, single sites. In the case of the IkBα inhibitor of the NF-kB transcriptional regulator, phosphorylation at two specific sites, Ser-32 and Ser-36, is required for ubiquitin ligation. β-cateinin, which is targeted for ubiquitin-mediated degradation by phosphorylation, has a sequence motif similar to that of IkBα around these phosphorylation sites. However, the homology in phosphorylation patterns of these two proteins is not complete, because phosphorylation of other sites of β-catenin is also required for its degradation. Other proteins targeted for degradation by phosphorylation include the Cdk inhibitor Sic1p and the STAT1 transcription factor. Though different patterns of phosphorylation target different proteins for degradation, a common feature appears to be that the initial regulatory event is carried out by a protein kinase, while the role of a ubiquitin ligase would be to recognize the phosphorylated form of the protein substrate. It further appears that different ubiquitin ligases recognize different phosphorylation patterns as well as additional motifs in the various protein substrates. However, the identity of such E3s is unknown, except for some PULC-type ubiquitin ligases that act on some phosphorylated cell-cycle regulators in the budding yeast. The multiplicity of signals that target proteins for ubiquitin-mediated degradation (and of ligases that have to recognize such signals) is underscored by observations that the phosphorylation of some proteins actually prevents their degradation. Thus the phosphorylation of the c-Mos protooncogene on Ser3 and the multiple phosphorylations of c-Fos and c-Jun protooncogenes at multiple sites by MAP kinases suppress their ubiquitinylation and degradation.
In addition to the families of enzymes involved in conjugation of ubiquitin, a very large family of deubiquitinating enzymes has recently been identified from various organisms. These enzymes have several possible functions. First, they may have peptidase activity and cleave the products of ubiquitin genes. Ubiquitin is encoded by two distinct classes of genes. One is a polyubiquitin gene, which encodes a linear polymer of ubiquitins linked through peptide bonds between the C-terminal Gly and N-terminal Met of contiguous ubiquitin molecules. Each copy of ubiquitin must be released by precise cleavage of the peptide bond between Gly-76-Met-1 of successive ubiquitin moieties. The other class of ubiquitin genes encodes ubiquitin C-terminal extension proteins, which are peptide bond fusions between the C-terminal Gly of ubiquitin and N-terminal Met of the extension protein. To date, the extensions described are ribosomal proteins consisting of 52 or 76–80 amino acids. These ubiquitin fusion proteins are processed to yield ubiquitin and the corresponding C-terminal extension proteins. Second, deubiquitinating enzymes may have isopeptidase activities. When a target protein is degraded, deubiquitinating enzymes can cleave the polyubiquitin chain from the target protein or its remnants. The polyubiquitin chain must also be disassembled by deubiquitinating enzymes during or after proteolysis by the 26 S proteasome, regenerating free monomeric ubiquitin. In this way, deubiquitinating enzymes can facilitate the ability of the 26 S proteasome to degrade ubiquitinated proteins. Third, deubiquitinating enzymes may hydrolyze ester, thiolester, and amide linkages to the carboxyl group of Gly-76 of ubiquitin. Such nonfunctional linkages may arise from reactions between small intracellular compounds such as glutathione and the E1-, E2-, or E3-ubiquitin thiolester intermediates. Fourth, deubiquitinating enzymes may compete with the conjugating system by removing ubiquitin from protein substrates, thereby rescuing them from degradation or any other function mediated by ubiquitination. Thus generation of ubiquitin by deubiquitinating enzymes from the linear polyubiquitin and ubiquitin fusion proteins and from the branched polyubiquitin ligated to proteins should be essential for maintaining a sufficient pool of free ubiquitin. Many deubiquitinating enzymes exist, suggesting that these deubiquitinating enzymes recognize distinct substrates and are therefore involved in specific cellular processes. Although there is recent evidence to support such specificity of these deubiquitinating enzymes, the structure-function relationships of these enzymes remain poorly studied.
Deubiquitinating enzymes can be divided broadly on the basis of sequence homology into two classes, the ubiquitin-specific processing protease (UBP or USP, also known as type 2 ubiquitin C-terminal hydrolase (type 2 UCH)) and the UCH, also known as type 1 UCH). UCH (type 1 UCH) enzymes hydrolyze primarily C-terminal esters and amides of ubiquitin but may also cleave ubiquitin gene products and disassemble polyubiquitin chains. They have in common a 210-amino acid catalytic domain, with four highly conserved blocks of sequences that identify these enzymes. They contain two very conserved motifs, the CYS and HIS boxes. Mutagenesis studies revealed that the two boxes play important roles in catalysis. Some UCH enzymes have significant C-terminal extensions. The functions of the C-terminal extensions are still unknown but appear to be involved in proper localization of the enzyme. The active site of these UCH enzymes contains a catalytic triad consisting of cysteine, histidine, and aspartate and utilizes a chemical mechanism similar to that of papain. The crystal structure of one of these, UCH-L3, has been solved at 1.8 Å resolution. The enzyme comprises a central antiparallel β-sheet flanked on both sides by helices. The β-sheet and one of the helices are similar to those observed in the thiol protease cathepsin B. The similarity includes the three amino acid residues that comprise the active site, Cys95, His169, and Asp184. The active site appears to fit the binding of ubiquitin that may anchor also at an additional site. The catalytic site in the free enzyme is masked by two different segments of the molecule that limit nonspecific hydrolysis and must undergo conformational rearrangement after substrate binding.
UBP (type 2 UCH) enzymes are capable of cleaving the ubiquitin gene products and disassembling polyubiquitin chains after hydrolysis. It appears that there is a core region of about 450 amino acids delimited by CYS and HIS boxes. Many of these isoforms have N-terminal extensions and a few have C-terminal extensions. In addition, there are variable sequences in the core region of many of the isoforms. The functions of these divergent sequences remain poorly characterized. Another interesting function of specific UBPs is the regulation of cell proliferation. It was observed that cytokines induced in T-cells specific deubiquitinating enzymes (DUBs), termed DUB-1 and DUB-2 DUB-1 is induced by stimulation of the cytokine receptors for IL-3, IL-5, and GM-CSF, suggesting a role in its induction for the β-common (betac) subunit of the interleukin receptors. Overexpression of a dominant negative mutant of JAK2 inhibits cytokine induction of DUB-1, suggesting that the regulation of the enzyme is part of the cell response to the JAK/STAT signal transduction pathway. Continued expression of DUB-1 arrests cells at G1; therefore, the enzyme appears to regulate cellular growth via control of the G0–G1 transition. The catalytic conserved Cys residue of the enzyme is required for its activity. DUB-2 is induced by IL-2 as an immediate early (IE) gene that is down-regulated shortly after the initiation of stimulation. The function of this enzyme is also obscure. It may stimulate or inhibit the degradation of a critical cell-cycle regulator.
Cytokines, such as interleukin-2 (IL-2), activate intracellular signaling pathways via rapid tyrosine phosphorylation of their receptors, resulting in the activation of many genes involved in cell growth and survival. The deubiquitinating enzyme DUB-2 is induced in response to IL-2 and is expressed in human T-cell lymphotropic virus-I (HTLV-1)-transformed T cells that exhibit constitutive activation of the IL-2 JAK/STAT (signal transducers and activators of transcription) pathway, and when expressed in Ba/F3 cells DUB-2 markedly prolonged IL-2-induced STAT5 phosphorylation. Although DUB-2 does not enhance IL-2-mediated proliferation, when withdrawn from growth factor, cells expressing DUB-2 had sustained STAT5 phosphorylation and enhanced expression of IL-2-induced genes cis and c-myc. DUB-2 expression markedly inhibited apoptosis induced by cytokine withdrawal allowing cells to survive. Therefore, DUB-2 has a role in enhancing signaling through the JAK/STAT pathway, prolonging lymphocyte survival, and, when constitutively expressed, may contribute to the activation of the JAK/STAT pathway observed in some transformed cells. (Migone, T.-S., et al., Blood. 2001;98:1935–1941).
Protein ubiquitination is an important regulator of cytokine-activated signal transduction pathways and hematopoietic cell growth. Protein ubiquitination is controlled by the coordinate action of ubiquitin-conjugating enzymes and deubiquitinating enzymes. Recently a novel family of genes encoding growth-regulatory deubiquitinating enzymes (DUB-1 and DUB-2) has been identified. DUBs are immediate-early genes and are induced rapidly and transiently in response to cytokine stimuli. By means of polymerase chain reaction amplification with degenerate primers for the DUB-2 complementary DNA, 3 murine bacterial artificial chromosome (BAC) clones that contain DUB gene sequences were isolated. One BAC contained a novel DUB gene (DUB-2A) with extensive homology to DUB-2. Like DUB-1 and DUB-2, the DUB-2A gene consists of 2 exons. The predicted DUB-2A protein is highly related to other DUBs throughout the primary amino acid sequence, with a hypervariable region at its C-terminus. In vitro, DUB-2A had functional deubiquitinating activity; mutation of its conserved amino acid residues abolished this activity. The 5′ flanking sequence of the DUB-2A gene has a hematopoietic-specific functional enhancer sequence. It is proposed that there are at least 3 members of the DUB subfamily (DUB-1, DUB-2, and DUB-2A) and that different hematopoietic cytokines induce specific DUB genes, thereby initiating a cytokine-specific growth response. (Baek , K.-H., et al, Blood. 2001;98:636–642).
Protein ubiquitination also serves regulatory functions in the cell that do not involve proteasome-mediated degradation. For example, Hicke and Riezman have recently demonstrated ligand-inducible ubiquitination of the Ste2 receptor in yeast. Ubiquitination of the Ste2 receptor triggers receptor endocytosis and receptor targeting to vacuoles, not proteasomes. Also, Chen et al. have demonstrated that activation of the IB kinase requires a rapid, inducible ubiquitination event. This ubiquitination event is a prerequisite for the specific phosphorylation of IB and does not result in subsequent proteolysis of the kinase complex. The ubiquitination of Ste2 and IB kinase appears reversible, perhaps resulting from the action of a specific deubiquitinating enzyme.
A large superfamily of genes encoding deubiquitinating enzymes, or UBPs, has recently been identified. UBPs are ubiquitin-specific thiol-proteases that cleave either linear ubiquitin precursor proteins or post-translationally modified proteins containing isopeptide ubiquitin conjugates. The large number of UBPs suggests that protein ubiquitination, like protein phosphorylation, is a highly reversible process that is regulated in the cell.
Interestingly, UBPs vary greatly in length and structural complexity, suggesting functional diversity. While there is little amino acid sequence similarity throughout their coding region, sequence comparison reveals two conserved domains. The Cys domain contains a cysteine residue that serves as the active enzymatic nucleophile. The His domain contains a histidine residue that contributes to the enzyme's active site. More recent evidence demonstrates six homology domains contained by all members of the ubp superfamily. Mutagenesis of conserved residues in the Cys and His domains has identified several residues that are essential for UBP activity.
Recently, a growth regulatory deubiquitinating enzyme, DUB-1, that is rapidly induced in response to cytokine receptor stimulation was identified. DUB-1 is specifically induced by the receptors for IL-3, granulocyte macrophage-colony-stimulating factor, and IL-5, suggesting a specific role for the c subunit shared by these receptors. In the process of cloning the DUB-1 gene, a family of related, cross-hybridizing DUB genes was identified. From this, other DUB genes might be induced by different growth factors. Using this approach, an IL-2-inducible DUB enzyme, DUB-2 and closely related DUB-2a were identified. DUB-1 and DUB-2 are more related to each other than to other members of the ubp superfamily and thereby define a novel subfamily of deubiquitinating enzymes.
Hematopoietic-specific, cytokine induced DUBs in murine system have shown to prolong cytokine receptor, see Migone, T. S., et al. (2001). The deubiquitinating enzyme DUB-2 prolongs cytokine-induced signal transducers and activators of transcription activation and suppresses apoptosis following cytokine withdrawal, Blood 98, 1935–41; Zhu, Y., et al., (1997). DUB-2 is a member of a novel family of cytokine-inducible deubiquitinating enzymes, J Biol Chem 272, 51–7 and Zhu, Y., et al., (1996). The murine DUB-1 gene is specifically induced by the betac subunit of interleukin-3 receptor, Mol Cell Biol 16, 4808–17.). These effects are likely due to the deubiquitination of receptors or other signaling intermediates by DUB-1 or DUB-2, murine analogs of hDUBs. Inhibition of hDUBs may achieve downregulation of specific cytokine receptor signaling, thus modulating specific immune responses.
Cytokines regulate cell growth by inducing the expression of specific target genes. A recently identified a cytokine-inducible, immediate-early gene, DUB-1, encodes a deubiquitinating enzyme with growth regulatory activity. In addition, a highly related gene, DUB-2, that is induced by interleukin-2 was identified. The DUB-2 mRNA was induced in T cells as an immediate-early gene and was rapidly down-regulated. Like DUB-1, the DUB-2 protein had deubiquitinating activity in vitro. When a conserved cysteine residue of DUB-2, required for ubiquitin-specific thiol protease activity, was mutated to serine (C60S), deubiquitinating activity was abolished. DUB-1 and DUB-2 proteins are highly related throughout their primary amino acid sequence except for a hypervariable region at their COOH terminus. Moreover, the DUB genes co-localize to a region of mouse chromosome 7, suggesting that they arose by a tandem duplication of an ancestral DUB gene. Additional DUB genes co-localize to this region, suggesting a larger family of cytokine-inducible DUB enzymes. We propose that different cytokines induce specific DUB genes. Each induced DUB enzyme thereby regulates the degradation or the ubiquitination state of an unknown growth regulatory factor, resulting in a cytokine-specific growth response.
On the basis of these structural criteria, additional members of the DUB subfamily can be identified in the GenBankTM. The highest degree of homology is in the Cys and His domains. Additionally, this putative human DUB protein contains a Lys domain (amino acids 400–410) and a hypervariable region (amino acids 413–442).
Murine DUB (mDUB) subfamily members differ from other UBPs by functional criteria as well. mDUB subfamily members are cytokine-inducible, immediate-early genes and may therefore play regulatory roles in cellular growth or differentiation. Also, DUB proteins are unstable and are rapidly degraded by ubiquitin-mediated proteolysis shortly after their induction.
mDUB reports demonstrate that specific cytokines, such as IL-2 and IL-3, induce specific deubiquitinating enzymes (DUBs). The DUB proteins may modify the ubiquitin-proteolytic pathway and thereby mediate specific cell growth or differentiation signals. These modifications are temporally regulated. The DUB-2 protein, for instance, is rapidly but transiently induced by IL-2. Interference of DUB enzymes with specific isopeptidase inhibitors may block specific cytokine signaling events.
Defensins constitute a major family of antimicrobial peptides in mammals. Depending on the distribution of the cysteines and the linkages of the disulfide bonds, human defensins can be divided into two categories: α-defensins, which can be found in granulocytes and in epithelial cells of the small intestine, and β-defensins, which are expressed by epithelial cells and leukocytes including macrophages. Some defensins are expressed constitutive manner in granulocytes and epithelial cells where as others are induces by either exposure to microbial pathogens or pro-inflammatory cytokines such as IL-1β, TNF-α and interferon-γ. The genes coding for human defensins are clustered within 1 Mb segment on chromosome 8P23, and it has been suggested that β-defensins may predate the a-defensin family during recent gene amplification since α-defensin cannot be detected even in many mammalians including cow. Cow has at least 13 β-defensins but no α-defensin. β-defensins contribute to early host defense against several bacterial and fungal pathogens, as an important mechanism of innate immune response. Beside this antimicrobial activity, a chemoattractant activity on both immature dentritic cells and memory T cells, as well as monocytes, has been recently described, demonstrating that β-defensins may promote both innate and adaptive immune response.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1: Proposed enzyme reaction mechanism of DUB-.



SUMMARY OF THE INVENTION
The present invention is directed to analogs of murine DUBs, hematopoietic-specific, cytokine-inducible deubiquitinating proteases found as a cluster of genes on chromosomes 4 and 8 and respective regulatory regions. Eleven novel human DUBs and four potential genes that express truncated form of DUBs not previously reported in public databases were identified by searching human genome database using murine DUB-1 and DUB-2 sequences. These genes share open reading frames (ORFs) that are 88 to 99% amino acid identity to each other, when gaps caused by deletion and N-terminal and/or C-terminal extension was not counted as mismatch, and exhibit approximately 50% identity to murine DUBs. Eight of eleven ORFs generate a protein of 530 amino acids. Two ORFs (hDUB8.3 and hDUB8.11) have internal in-frame deletions such that the genes are capable of generating 497 and 417 amino acid long polypeptides, respectively. One ORF (hDUB4.5) exhibits extension at both 5′ and 3′ end of the ORF so that the gene is capable of expressing 574 amino acid long polypeptide. Surprisingly, this 5′ extension results in specific pro-polypeptide sequence that can direct polypeptide targeting to the mitochondria. Furthermore, the respective regulatory regions, putative promoters, of these genes also share close to 90% identity each other suggesting that their expression is coordinated. In addition, we found that two of these genes can be expressed under the control of separate promoters that can be controlled independently and expressing potentially distinctive protein products.
Manipulation of these gene products by small molecular compounds can (1) reduce inflammation by regulating proinflammatory cytokine signaling, (2) modulate autoimmune diseases by regulating cytokine receptor signaling that are critical for lymphocytes proliferation, and (3) immune over-reaction during infection using above mechanisms.
Two of cluster genes (hDUB4.1 and hDUB4.2) possesses two distinctive promoter domains in front of their ORFs such that they can be regulated independently in their transcription potential. The longer transcripts of these ORFs (called hDUB4.1a and hDUB4.2a) has 12 and 4 exons respectively and capable of generating 1016 and 1021 amino acid long polypeptides, respectively. These polypeptides share C-terminal 530 amino acids with their shorter form that can be expressed separately from independent promoters (called hDUB4.1b and hDUB4.2b, respectively). In addition, two other ORFs are capable of generating longer than 530 amino acid polypeptides (hDUB4.10 and hDUB4.11). Remarkably, these two deduced polypeptides shares significant homology within portion of N-terminal portions (I added alignment file of these at the end of sequence file). Three of the ORFs (hDUB4.5, 4.8, and 8.2) has N-terminal insertion that is typical for mitochondria targeting sequence. An alignment of these sequences is provide in the Tables. The promoter sequences defined as upstream of initiation ATG of the ORF exhibit remarkable level of homology each other except that of hDUB4.1a. The sequence identity among all promoter sequences except that of hDUB4.1a is approximately 90% in 2000 base pair span upstream of initiation ATG. Two of the promoter sequences (hDUB8.3 and 8.11) have 334 nucleotides insertion at approximately 1000 base pair upstream of initiation ATG. Interestingly, hDUB8.3 and hDUB8.11 are the only ones with shorter ORFs due to the internal deletions. In addition to these ORFs, there are 5 ORFs that are capable of expressing polypeptides (hDUB4.4, hDUB4.9, hDUB8.2, hDUB8.9, and hDUB8.10) that share initiation codon with other 530 amino acid long polypeptides but terminate prematurely due to the in frame termination sequences. These also shares significant homology upstream of ATG initiation codon suggesting they may expressed as truncated proteins, potential regulatory functions. All 11 hDUB8 genes are clustered with the defensin clusters within 2 Mb region in 8P23, implying that both acquisition and amplification are relatively recent event, perhaps during mammalian evolution. It is of interest that hDUB4 gene cluster is also in highly amplified cluster region of chromosome 4P16 that is yet to be assigned in chromosome location. These data suggest that hDUB4s and hDUB8s are within very dynamic region of the human chromosomes (both 4p16 and 8p23) that are undergoing volatile amplifications. The data also suggest that expression of hDUB8 may also be coordinated in conjunction with defensins that are critical components of innate immune response and inflammation.
Search Methods for Identifying Human Analogs of mDUBs:
In order to identify human analogs of mDUB1, -2, -2A, mDUB1 (U41636), mDUB2 (NM—010089), and mDUB2A (AF393637) DNA sequences were used to search against Ensembl entire “golden path” (as contigs) using Ensembl blast search engine (http://www.ensembl.org/perl/blastview). All three mDUBs have significant alignments with contig AC083981, AF252831, AF228730, AF252830, AC068974 on chromosome 8 with the high score above 2000 and the probability less than e-87. In order to find all the homolog genes in the genome, exhaust search was performed using genomic aligned sequence to search against the “golden path” contigs. Two more contigs were found to have significant alignment that has probability less than e-100: one is AC074340 on chromosome 8 and the other is AC022770 on chromosome 4.
DNA sequences for contig AC083981, AF252831, AF228730, AF252830, AC068974, AC074340 and AC022770 were downloaded from Ensembl and gene annotation for each contig was performed using GenScan gene annotation program. Genes having homolog with mDUBs were named in sequence based on their locations on chromosomes. For example, hDUB8.1 was derived from AF228730, 8.2, 8.3 were derived from AF252830, 8.5 were derived from AC074340, 8.6 were derived from AF252831, 8.7, 8.8 and 8.9 were derived from AC083981, and 8.10 and 8.11 were derived from AC068974. hDUB4.1, 4.2, 4.3, 4.4, 4.5 were derived from AC022770 on chromosome 4.
Using these hDUB4s and hDUB8s, both Ensemble and NCBI blast search was performed. Further contig NT—028165 that covers chromosome 4 was identified. From this and already assembled chromosome 4p16.1 region, further annotation was performed using GenScan gene annotation program. From this we identified hDUB4.6, 4.7, 4.8, 4.9, 4.10, and 4.11.
Analysis of the hDUB gene clusters in chromosome 4 reveals that at least five ORFs in an unmapped cOntig (AC022770) were identified by nucleotide homology search with murine DUB1 and 2. At least four out of five ORFs share core 530 amino acid sequences. Two ORFs (hDUB4.1 and hDUB4.2) are multi-exon ORFs that extend N-terminal part of polypeptides that shares minimal sequence identity. However, there is a conserved putative promoter sequences that encompass over 2,000 bases in the intron region proximal to the last exon that is conserved among all 5 genes. Three of the ORFs (hDUB4.5, 4.8, and 8.2) has N-terminal insertion that is typical for mitochondria targeting sequence. The hDUB genes cluster in 4P16 of the human chromosome, which is an unmapped part of the human chromosome.
Analysis of the hDUB gene clusters in chromosome 8 reveals that at least eleven ORFs in six different contigs (AC068974, AC074340, AC083981, AF228730, AF252830, and AF252831) were identified by nucleotide homology search with murine DUB1 and 2. At least seven out of eleven ORFs share significant identities with similar length. There are conserved putative promoter sequences that encompass over 2,000 bases in all 11 genes. The hDUB genes cluster in 8P23.1 of the human chromosome and clustered with defensin molecules (at lease 9 defensins are clustered with hDUB8s) and the whole domain belongs the olfactory GPCR cluster.
Analysis of the deduced amino acid sequences of the hDUBs reveals polypeptides consistent with mDUBs, which contain highly conserved Cys and His domains that are likely to form the enzyme's active site. The putative active site nucleophile of mDUB-2 is a cysteine residue (Cys−60) in the Cys domain. Both mDUB-1 and mDUB-2 have a lysine rich region (Lys domain; amino acids 374–384 of mDUB-2) and a short hypervariable region (amino acids 385–451 of mDUB-2), in which the mDUB-1 and mDUB-2 sequences diverge considerably. The hypervariable (HV) region of mDUB-2 contains a duplication of the eight-amino acid sequence: PQEQNHQK (Seq ID No. 55).
The protein and nucleotide sequences named in this invention and their Sequence ID NOs are set forth as following:
Nucleotide Sequence for hDUB4.1a: Seq ID No. 3
hDUB4.1a deduced polypeptide sequence: Seq ID No. 4
Nucleotide Sequence for hDUB4.1b: Seq ID No. 5
hDUB4.1b deduced polypeptide sequence: Seq ID No. 6
Nucleotide Sequence for hDUB4.2a: Seq ID No. 7
hDUB4.2a deduced polypeptide sequence: Seq ID No. 8
Nucleotide Sequence for hDUB4.2b: Seq ID No. 9
hDUB4.2b deduced polypeptide sequence: Seq ID No. 10
Nucleotide Sequence for hDUB4.3: Seq ID No. 11
hDUB4.3 deduced polypeptide sequence: Seq ID No. 12
Nucleotide Sequence for hDUB4.5: Seq ID No. 13
hDUB4.5 deduced polypeptide sequence: Seq ID No. 14
Nucleotide Sequence for hDUB4.6: Seq ID No. 15
hDUB4.6 deduced polypeptide sequence: Seq ID No. 16
Nucleotide Sequence for hDUB4.7: Seq ID No. 17
hDUB4.7 deduced polypeptide sequence: Seq ID No. 18
Nucleotide Sequence for hDUB4.8: Seq ID No. 19
hDUB4.8 deduced polypeptide sequence: Seq ID No. 20
Nucleotide Sequence for hDUB4.10: Seq ID No.21
hDUB4.10 deduced polypeptide sequence: Seq ID No. 22
Nucleotide Sequence for hDUB4.11: Seq ID No. 23
hDUB4.11 deduced polypeptide sequence: Seq ID No. 24
Nucleotide Sequence for hDUB8.1: Seq ID No. 25
hDUB8.1 deduced polypeptide sequence: Seq ID No. 26
Nucleotide Sequence for hDUB8.3: Seq ID No. 27
hDUB8.3 deduced polypeptide sequence: Seq ID No. 28
Nucleotide Sequence for hDUB8.5: Seq ID No. 29
hDUB8.5 deduced polypeptide sequence: Seq ID No. 30
Nucleotide Sequence for hDUB8.6: Seq ID No. 31
hDUB8.6 deduced polypeptide sequence: Seq ID No. 32
Nucleotide Sequence for hDUB8.7: Seq ID No. 33
hDUB8.7 deduced polypeptide sequence: Seq ID No. 34
Nucleotide Sequence for hDUB8.8: Seq ID No. 35
hDUB8.8 deduced polypeptide sequence: Seq ID No. 36
Nucleotide Sequence for hDUB8.11: Seq ID No. 37
hDUB8.11 deduced polypeptide sequence: Seq ID No. 38
Nucleotide Sequence for hDUB4.4: Seq ID No. 39
hDUB4.4 deduced polypeptide sequence: Seq ID No. 40
Nucleotide Sequence for hDUB4.9: Seq ID No. 41
hDUB4.9 deduced polypeptide sequence: Seq ID No. 42
Nucleotide Sequence for hDUB8.2: Seq ID No. 43
hDUB8.2 deduced polypeptide sequence: Seq ID No. 44
Nucleotide Sequence for hDUB8.9: Seq ID No. 45
hDUB8.9 deduced polypeptide sequence: Seq ID No. 46
Nucleotide Sequence for hDUB8.10: Seq ID No. 47
hDUB8.10 deduced polypeptide sequence: Seq ID No. 48
Promoter sequence for hDUB4.6: Seq ID No. 49
Promoter sequence for hDUB4.7: Seq ID No. 50
Promoter sequence for hDUB4.8: Seq ID No. 51
Promoter sequence for hDUB4.9: Seq ID No. 52
Promoter sequence for hDUB4.10: Seq ID No. 53
Promoter sequence for hDUB4.11: Seq ID No. 54
TaqMan Real Time PCR Analysis of Expression of hDUB4s and hDUB8s in Human Immunocytes upon Various Stimulation
Protocol of Reverse Transcription (RT) from Total Cellular RNA using Random Hexamer as Primer (using TaqMan Reverse Transcription Reagents Cat# N808-0234)
1 ug of total RNA preparation in 100 ul of 1×TaqMan RT Buffer Mix, 5.5 mM MgCl2, 0.5 mM dNTPs, 2.5 uM Random Hexamers, 40 U RNAse inhibitor, 125 U Multiscribe Reverse Transcriptase. Mix by pipeting up and down. Incubate 25° C. for 10 minutes (annealing step), 48° C. for 30 minutes (reverse transcription), and 95° C. for 5 minutes (heat killing of the enzyme). The samples can be left at the machine at 4° C., or alternatively, can be stored at −20° C. Yield of cDNA synthesis can be measured by incorporation of small portion of radioactive dATP (or dCTP). Average efficiency for this protocol is between 60–80% of conversion of RNA to cDNA.
Protocol of TaqMan Real-Time Quantitative PCR
1 ul of TaqMan RT product in 12.5 ul of 1× master Mix (Applied Biosystems Cat# 4304437) containing all necessary reaction components except primers and probes, 0.9 uM forward primer, 0.9 uM reverse primer, 0.2 uM probe. Mix by pipetting up and down. Samples containing GADPH primer pair and probe were also prepared as control. Thermal cycling and detection of the real-time amplification were performed using the ABI PRISM 7900HT Sequuence Detection System. The quantity of target gene is given relative to the GADPH control based on Ct values determined during the exponential phase of PCR.
Primer-probe Sets used and their Specificities:

    
    
        Primer 4.1 is unique for hDUB 4.1
        Primer 4.2 covers hDUB 4.2, 4.3, 4.5 and 8.1
        Primer 8.3 covers hDUB 8.3 and 8.11
        Primer 8.5 is unique for hDUB 8.5
        Primer 8.6 covers hDUB 8.6, 8.7 and 8.8
    
    









TABLE 1







Expression of hDUBs in PBMC stimulated with LPS (100 ng/ml)


and PHA (5 ug/ml) for 7 hours.










Donor 1












Fold-

Donor 2












Upregulation
Relative
Fold-Upregulation
Relative


Primer
upon stimulation
expression
upon stimulation
expression














4.1
2.2
1
3.8
1


4.2
2.0
21000
2.0
16400


8.3
1.8
5560
1.8
5500


8.5
2.1
80
3.1
310


8.6
2.6
19200
3.0
23000
















TABLE 2







Expression of hDUBs in PBMC stimulated with LPS (100 ng/ml)


for 1.5, 7 and 24 hours (Donor 3)











1.5 hours
7 hours
24 hours














Fold-








Upregula-
Rela-
Fold-
Rela-
Fold-
Rela-



tion upon
tive
Upregulation
tive
Upregulation
tive



stimula-
express-
upon
express-
upon
express-



tion
ion
stimulation
ion
stimulation
ion

















4.2
2.4
64
336
35.2
1.8
12.5


8.3
0.4
1
13.1
1
1.7
1


8.5
1.6
11
65.9
4.8
1.5
1.8
















TABLE 3







Expression of DUBs in PBMC stimulated with LPS (100 ng/ml) and/or PHA (5


ug/ml) for 1.5, 7, 24 hours (donor 4)











1.5 hours
7 hours
24 hours
















Fold-

Fold-

Fold-





Upregulation

Upregulation

Upregulation





upon
Relative
upon
Relative
upon
Relative



Primer
stimulation
expression
stimulation
expression
stimulation
expression


















LPS
4.2
0.4
39
2.5
54
1.6
48



8.3
0.5
5
1.6
6
1.1
7



8.5
0.9
1
1.5
1.7
1.4
2



8.6
0.6
26
1.7
57
1.0
21


PHA
4.2
3.5
367
4.4
94
0.9
26



8.3
1.5
13
1.7
6
0.7
5



8.5
1.9
2
0.9
1
0.7
1



8.6
2.3
103
2.5
23
0.8
17


LPS +
4.2
1.2
129
3.4
73
0.8
23


PHA
8.3
1.0
9
2.2
8
0.7
5



8.5
1.0
1
0.9
1.3
0.9
1.2



8.6
1.3
56
2.5
33
0.8
18









There is no increase of expression in T lymphocytes (donor 5) and B lymphocytes (donor 6) when stimulated with anti-CD4/CD28 and anti-CD40/IL-4, respectively.








TABLE 4







Expression of hDUB 4.2, 4.3, 4.5 and 8.1 examined by primer


4.2 in different human organ panel by TaqMan analysis.











Tissue Type
Mean
β 2 Mean
∂∂ Ct
Expression














Adrenal Gland
29.72
20.00
10.08
0.92


Bone marrow
34.02
20.49
13.89
0.07


Brain
26.92
22.73
4.54
42.84


Colon
32.03
19.97
12.42
0.18


Fetal Brain
27.59
24.23
3.71
76.15


Fetal Liver
33.22
22.58
10.99
0.49


Heart
33.09
21.60
11.85
0.27


Kidney
29.93
21.97
8.32
3.13


Lung
32.10
19.31
13.15
0.11


Mammary Gland
30.00
21.74
8.61
2.56


Pancreas
34.83
24.07
11.11
0.45


Placenta
36.60
23.77
13.19
0.00


Prostate
29.14
20.93
8.55
2.66


Salivary Gland
32.11
21.39
11.07
0.46


Skeletal Muscle
28.27
20.44
8.18
3.45


Small Intestine
34.33
21.00
13.69
0.08


Spinal Cord
27.04
21.91
5.47
22.48


Spleen
32.45
19.02
13.78
0.07


Stomach
32.15
21.66
10.84
0.55


Testis
28.57
23.07
5.87
17.16


Thymus
31.01
20.68
10.69
0.61


Thyroid
28.84
20.80
8.39
2.97


Trachea
31.39
19.63
12.11
0.23


Uterus
30.37
21.09
9.64
1.25


PBMC/Control
33.98
18.82
15.52
0.02


PBMC/PMA
33.62
18.81
15.17
0.03


PBMC/PHA
34.20
18.77
15.78
0.02


PBMC/HDM
34.23
17.81
16.77
0.01


A549 Cells
31.98
21.57
10.77
0.57


THP-1
35.48
20.75
15.09
0.00


Ovary
31.84
21.55
10.65
0.62


(+ve) Positive Control
29.61
21.86
8.11
3.62
















TABLE 5







Expression of hDUB 4.2, 4.3, 4.5 and 8.1 examined


by primer 4.2 in human immunocytes panel:











Cell Type and stimulation

β 2




condition
Mean
Mean
∂∂ Ct
Expression














Granulocyte resting
34.18
17.22
17.50
0.005


Granulocyte TNF-β 4/24 hr
32.39
17.16
15.76
0.018


CD19 (tonsillar-CD40L)
28.7
19.92
9.32
1.565


CD19 (tonsillar-LPS)
31.14
20.67
11.00
0.488


FLS-REST
34.67
20.43
14.78
0.036


FLS-IL1 4/24 hr
34.26
20.41
14.38
0.047


FLS-TNF-β 4/24 hr
34.91
20.15
15.31
0.025


Monocyte resting (pool 1.5, 7,
33.63
18.29
15.89
0.017


24 hr)


Monocyte LPS (pool 1.5, 7, 24 hr)
34.55
18.03
17.06
0.007


Monocyte INF-g (pool 1.5, 7,
34.62
17.27
17.88
0.004


24 hr)


Monocyte LPS & IFN-β (pool
34.87
17.38
18.03
0.004


1.5, 7, 24 hr)


DCs progenitors (CD14+)
35.87
19.73
16.67
0.000


DCs immature
35.48
18.18
17.84
0.000


DCs mature
37.46
17.92
20.07
0.000


TH0 resting
31.11
17.63
14.02
0.060


TH0 activated
31.29
18.23
13.60
0.081


Th1 resting
33.88
18.27
16.15
0.014


Th1 CD28/CD3
32.15
19.31
13.38
0.094


Th2 resting
33.94
18.07
16.40
0.012


Th2 CD28/CD3
33.27
18.78
15.02
0.030


BSMC
35.33
21.64
14.22
0.000


BSMC IL-4 + TNF-β 24 hr
36.44
21.52
15.45
0.000


BSMC IL-13 + TNF-β 24 hr
35.94
21.41
15.07
0.000


BSMC IL-4 + IL-13
36.28
22.09
14.73
0.000


NHBE d0
36.63
22.24
14.92
0.000


NHBE IL-4 + TNF-β d0
35.72
21.42
14.83
0.000


NHBE IL-13 + TNF-βd0
36.35
21.37
15.52
0.000


NHBE resting d7 + d14
34.89
22.41
13.01
0.121


NHBE IL-4 + TNF-β d7 + d14
38.59
22.02
17.11
0.000


NHBE IL-13 + TNF-β d7 + d14
37.62
21.93
16.23
0.000


CD8 T cell O hour
30.15
19.52
11.16
0.437


CD8 T cell a-CD3/CD28 4 hour
32.08
19.6
13.01
0.121


CD8 T cell a-CD3/CD28 24
30.94
18.64
12.84
0.137


hour


HMVEC resting
35.09
20.25
15.38
0.000


HMVEC TNF-β + IL-4 24 hr
35.91
20.86
15.59
0.000


HMVEC TNF-β 24 hr
35.57
21.06
15.05
0.000


HMVEC TNF-β + IL-13 24 hr
36.38
20.61
16.31
0.000


Normal synovium pool
34.92
21.16
14.3
0.050


RA synovium pool
33.65
20.88
13.3
0.099


Normal colon
32.5
21.68
11.36
0.381


Colitis Colon
33.17
21.32
12.39
0.187


Crohns colon pooled
32.91
22.06
11.39
0.374


Normal Lung
31.01
20.5
11.05
0.472


COPD Lung
35.09
22.14
13.49
0.000


Positive control
28.4
22.29
6.64
9.992









Cloning of hDUB4,8s by PCR

Following promer set was used to clone 530 amino acid open reading frame portion of single exon hDUB4s and 8s from human genomic DNA:










N-terminal primer:




5′-atggaggacgactcactct-3′
(Seq ID No. 1)



 



C-terminal primer:



5′-ctggcacacaagcaga-3′
(Seq ID No. 2)






Underlined triplet nucleotides in each primer represent translational initiation and termination codon. This primer set can amplify most of hDUB4s and hDUB8s as well as potentially yet to be identified hDUBs that are similar enough to hDUB4s and hDUB8s due to the high homology in nucleotide sequences in this part of the ORF. 1593 base pair fragment was successfully amplified from genomic DNA from two healthy human subjects and cloned into pCR2.1 vector and transformed into TOP10 strain of E coli. Over 300 independent clones with appropriate size insert were obtained and sequences are obtained by ABI automated DNA sequencers.

Deubiquitination Assay

Confirmation that the DUB is a deubiquitinating enzyme may be shown using previously identified deubiquitination assay of ubiquitin-galactosidase fusion proteins, as described previously in the literature. Briefly, a fragment of the DUB, of approximately 1,500 nucleotides, based on the wild-type DUB cDNA (corresponding to amino acids 1 to about 500) and a cDNA containing a missense mutation are generated by PCR and inserted, in frame, into pGEX (Pharmacia), downstream of the glutathione S-transferase (GST) coding element. Ub-Met-gal is expressed from a pACYC184-based plasmid. Plasmids are co-transformed as indicated into MC1061 Escherichia coli. Plasmid-bearing E. coli MC1061 cells are lysed and analyzed by immunoblotting with a rabbit anti-gal antiserum (Cappel), a rabbit anti-GST antiserum (Santa Cruz), and the ECL system (Amersham Corp.). in vitro deubiquitinating enzyme activity may be shown from purified hDUB fusion protein using commercial polyubiquitinated protein as substrate.
HDUB4s and hDUB8s are Potential Inflamatory Cytokins Specific Immediate-early Genes
mDUB-1 was originally cloned as an IL-3-inducible immediate-early gene. Similarly, mDUB-2 was cloned as an IL-2-inducible immediate-early gene. We examined inducibility as well as cell-type specific expression of these genes using multiple TaqMan analysis from human organ RNA samples and human immunocytes RNA samples. Our data suggest that expression of hDUBs are not apparent in lymphocytes and granulocytes but high in fresh human PBMC from several donor. This strongly suggest that expression may be limited to the monocytes/macrophages and potentially NK cells. hDUB4s and hDUB8s are upregulated in PBMC stimulated with stimuli (LPS and/or PHA) that is known to upregulate various inflammatory cytokines such as TNF-alpha, IL-1 beta etc. This increase of expression is almost completely disappeared 20 to 24 hours after stimulation suggesting this is an early gene. The fact that there is only weak expression upregulation at 1.5 hours after stimulation suggests that stimuli by themselves may not upregulate hDUB4s and hDUB8s, but cytokines that are upregulated within couple of hours after stimulation may be responsible for upregulation of the hDUB4s and hDUB8s.
The DUB Subfamily of the ubp Superfamily
From these data we propose that hDUB4s and hDUB8s are members of a discrete subfamily of deubiquitinating enzymes that shows the strongest similarity to mDUB subfamily including mDUB1, mDUB2, and mDUB2A, called the DUB subfamily. DUB subfamily members contain distinct structural features that distinguish them from other ubps. First, DUB subfamily members are comparatively small enzymes of approximately 500–550 amino acids. Second, DUB subfamily members share amino acid similarity not only in the Cys and His domains but also throughout their primary amino acid sequence. For instance, DUB proteins contain a lysine-rich region (Lys domain) and a HV domain near their carboxyl terminus.
The regulatory regions, or promoter regions, of each of the DUBs was analyzed for putative transcription factor binding motifs using TRANSFACFind, a dynamic programming method, see Heinemeyer, T., et al., “Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms” Nucleic Acids Res. 27, 318–322, (1999). The Transfac database provides eukaryotic cis- and trans-acting regulatory elements.







TABLE 6







putative transcription factor binding motifs within the


DUB regulatory or promoter, region of hDUB 4.1a.


The position is indicated by nucleotides.










Transfac
Position(Score)
Name
Description





M00271
729 . . . 724(100)
AML-1a
runt-factor AML-1


M00148
296 . . . 302(100)
SRY
sex-determining region Y gene product



1016 . . . 1010(96)



958 . . . 964(94)



474 . . . 480(94)



1982 . . . 1988(92)



129 . . . 123(90)



857 . . . 863(90)



776 . . . 782(90)



1919 . . . 1913(90)



1227 . . . 1233(90)



276 . . . 282(90)



1741 . . . 1735(90)



193 . . . 199(90)



105 . . . 111(90)


M00240
1600 . . . 1606(100)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman





homolog



700 . . . 694(100)


M00083
892 . . . 899(100)
MZF1
MZF1


M00101
162 . . . 156(100)
CdxA
CdxA



1008 . . . 1002(100)



423 . . . 429(100)



153 . . . 147(99)



359 . . . 353(98)



1388 . . . 1394(98)



1644 . . . 1650(97)



1702 . . . 1696(97)



250 . . . 256(97)



231 . . . 237(97)



617 . . . 611(94)



509 . . . 503(93)



432 . . . 426(92)



307 . . . 313(92)



153 . . . 159(92)



1832 . . . 1838(92)



1366 . . . 1372(92)



494 . . . 500(92)



1450 . . . 1456(91)



1456 . . . 1450(91)



722 . . . 716(90)



991 . . . 985(90)



986 . . . 992(90)



1646 . . . 1640(90)


M00253
1142 . . . 1149(97)
cap
cap signal for transcription initiation



1344 . . . 1351(96)



639 . . . 632(95)



1313 . . . 1320(94)



1872 . . . 1879(93)



269 . . . 262(92)



257 . . . 250(91)



1103 . . . 1110(91)



745 . . . 752(91)



1589 . . . 1596(90)


M00099
978 . . . 993(96)
S8
S8



1637 . . . 1652(94)



995 . . . 980(93)


M00100
162 . . . 156(96)
CdxA
CdxA



1008 . . . 1002(96)



423 . . . 429(96)



1774 . . . 1768(96)



415 . . . 421(92)



860 . . . 854(91)



1026 . . . 1020(91)



494 . . . 500(91)



94 . . . 100(91)


M00285
725 . . . 713(95)
TCF11
TCF11/KCR-F1/Nrf1 homodimers



982 . . . 970(92)


M00347
531 . . . 522(95)
GATA-1
GATA-binding factor 1


M00135
1642 . . . 1660(95)
Oct-1
octamer factor 1


M00075
217 . . . 226(94)
GATA-1
GATA-binding factor 1


M00278
530 . . . 522(94)
Lmo2
complex of Lmo2 bound to Tal-1, E2A proteins,





and GATA-1, half-site 2



900 . . . 908(90)


M00157
990 . . . 978(94)
RORalpha2
RAR-related orphan receptor alpha2


M00127
533 . . . 520(93)
GATA-1
GATA-binding factor 1


M00109
1933 . . . 1920(93)
C/EBPbeta
CCAAT/enhancer binding protein beta


M00190
1656 . . . 1643(93)
C/EBP
CCAAT/enhancer binding factor


M00137
1193 . . . 1205(93)
Oct-1
octamer factor 1



248 . . . 260(90)



1652 . . . 1640(90)


M00302
1501 . . . 1512(92)
NF-AT
Nuclear factor of activated T-cells


M00077
900 . . . 908(91)
GATA-3
GATA-binding factor 3



530 . . . 522(90)


M00126
533 . . . 520(91)
GATA-1
GATA-binding factor 1


M00159
1231 . . . 1219(91)
C/EBP
CCAAT/enhancer binding protein


M00074
1280 . . . 1292(91)
c-Ets-1(p54)
c-Ets-1(p54)


M00042
192 . . . 201(91)
Sox-5
Sox-5


M00241
1650 . . . 1643(91)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman





homolog


M00116
138 . . . 125(91)
C/EBPalpha
CCAAT/enhancer binding protein alpha


M00138
1640 . . . 1662(91)
Oct-1
octamer factor 1


M00128
532 . . . 520(90)
GATA-1
GATA-binding factor 1


M00248
1645 . . . 1656(90)
Oct-1
octamer factor 1


M00289
1009 . . . 1021(90)
HFH-3
HNF-3/Fkh Homolog 3 (= Freac-6)
















TABLE 7







transcription factor binding motifs within the DUB regulatory or promoter,


region of hDUB 4.1b (SEQ ID NO: 6). The position is indicated by nucleotides.










Transfac
Position(Score)
Name
Description





M00254
1831 . . . 1820(99)
CCAAT
cellular and viral CCAAT box


M00101
832 . . . 826(98)
CdxA
CdxA



727 . . . 721(92)



70 . . . 64(92)



570 . . . 564(92)



523 . . . 529(92)



425 . . . 431(92)



1682 . . . 1688(91)



1409 . . . 1415(91)



1415 . . . 1409(91)



1688 . . . 1682(91)


M00054
470 . . . 461(97)
NF-kappaB
NF-kappaB



643 . . . 634(95)


M00148
946 . . . 940(96)
SRY
sex-determining region Y gene product



1564 . . . 1570(92)



1528 . . . 1534(92)



1092 . . . 1098(92)



1048 . . . 1054(90)



708 . . . 714(90)



655 . . . 661(90)



1360 . . . 1354(90)



1824 . . . 1818(90)



396 . . . 390(90)



749 . . . 743(90)



1016 . . . 1010(90)



302 . . . 308(90)


M00053
470 . . . 461(95)
c-Rel
c-Rel



643 . . . 634(94)


M00285
1734 . . . 1746(95)
TCF11
TCF11/KCR-F1/Nrf1 homodimers



1111 . . . 1123(91)



17 . . . 5(90)


M00052
470 . . . 461(95)
NF-kappaB
NF-kappaB (p65)



643 . . . 634(94)


M00077
1933 . . . 1941(95)
GATA-3
GATA-binding factor 3


M00253
485 . . . 492(95)
cap
cap signal for transcription initiation



1893 . . . 1886(95)



749 . . . 756(94)



834 . . . 841(93)



1484 . . . 1477(92)



511 . . . 504(92)



1194 . . . 1201(91)



163 . . . 170(91)



321 . . . 328(91)



340 . . . 347(91)



1815 . . . 1808(90)



563 . . . 570(90)


M00096
652 . . . 660(95)
Pbx-1
Pbx-1


M00194
472 . . . 459(95)
NF-kappaB
NF-kappaB


M00209
1818 . . . 1831(94)
NF-Y
NF-Y binding site


M00116
1238 . . . 1225(94)
C/EBPalpha
CCAAT/enhancer binding protein alpha


M00203
1699 . . . 1689(94)
GATA-X
GATA binding site



1227 . . . 1217(90)


M00241
535 . . . 542(94)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman





homolog


M00033
759 . . . 746(94)
p300
p300



333 . . . 320(90)


M00127
1703 . . . 1690(93)
GATA-1
GATA-binding factor 1


M00158
323 . . . 310(93)
COUP-TF
COUP/HNF-4 heterodimer


M00075
1889 . . . 1898(93)
GATA-1
GATA-binding factor 1



142 . . . 133(90)



1736 . . . 1745(90)


M00286
963 . . . 976(93)
GKLF
gut-enriched Krueppel-like factor


M00278
1933 . . . 1941(93)
Lmo2
complex of Lmo2 bound to Tal-1, E2A proteins,





and GATA-1, half-site 2


M00076
1932 . . . 1941(93)
GATA-2
GATA-binding factor 2



983 . . . 992(92)


M00208
471 . . . 460(93)
NF-kappaB
NF-kappaB binding site


M00185
1829 . . . 1819(92)
NF-Y
nuclear factor Y (Y-box binding factor)


M00302
232 . . . 243(92)
NF-AT
Nuclear factor of activated T-cells


M00348
98 . . . 107(92)
GATA-2
GATA-binding factor 2


M00134
308 . . . 326(92)
HNF-4
hepatic nuclear factor 4


M00223
548 . . . 540(92)
STATx
signal transducers and activators of transcription


M00039
1046 . . . 1039(92)
CREB
cAMP-responsive element binding protein


M00271
1955 . . . 1960(92)
AML-1a
runt-factor AML-1


M00074
231 . . . 243(91)
c-Ets-1(p54)
c-Ets-1(p54)



252 . . . 264(91)


M00289
385 . . . 397(91)
HFH-3
HNF-3/Fkh Homolog 3 (= Freac-6)


M00199
1722 . . . 1714(91)
AP-1
AP-1 binding site


M00032
254 . . . 263(91)
c-Ets-1(p54)
c-Ets-1(p54)


M00147
782 . . . 773(91)
HSF2
heat shock factor 2


M00100
1101 . . . 1095(91)
CdxA
CdxA


M00042
650 . . . 659(90)
Sox-5
Sox-5


M00183
1026 . . . 1035(90)
c-Myb
c-Myb


M00240
963 . . . 957(90)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman





homolog



1272 . . . 1266(90)


M00190
1238 . . . 1225(90)
C/EBP
CCAAT/enhancer binding factor


M00083
49 . . . 42(90)
MZF1
MZF1


M00184
275 . . . 284(90)
MyoD
myoblast determining factor


M00087
980 . . . 991(90)
Ik-2
Ikaros 2


M00221
1860 . . . 1850(90)
SREBP-1
sterol regulatory element-binding protein 1


M00137
1388 . . . 1376(90)
Oct-1
octamer factor 1
















TABLE 8







putative transcription factor binding motifs within the DUB regulatory or promoter,


region of hDUB 4.2a. The position is indicated by nucleotides.










Transfac
Position(Score)
Name
Description





M00148
992 . . . 986(100)
SRY
sex-determining region Y gene product



942 . . . 948(100)



919 . . . 913(96)



1544 . . . 1550(92)



1505 . . . 1511(92)



815 . . . 809(90)



1068 . . . 1074(90)



1196 . . . 1190(90)



1337 . . . 1331(90)



680 . . . 686(90)



1697 . . . 1691(90)



1802 . . . 1796(90)



368 . . . 362(90)



721 . . . 715(90)



274 . . . 280(90)


M00100
1077 . . . 1071(100)
CdxA
CdxA


M00271
1933 . . . 1938(100)
AML-1a
runt-factor AML-1



2204 . . . 2209(92)


M00101
1077 . . . 1071(99)
CdxA
CdxA



805 . . . 799(98)



699 . . . 693(92)



1384 . . . 1390(92)



936 . . . 942(92)



495 . . . 501(92)



1660 . . . 1666(91)



1666 . . . 1660(91)


M00076
716 . . . 707(98)
GATA-2
GATA-binding factor 2



1910 . . . 1919(95)



959 . . . 968(92)



1679 . . . 1670(91)


M00285
1712 . . . 1724(96)
TCF11
TCF11/KCR-F1/Nrf1 homodimers



1087 . . . 1099(91)


M00272
1242 . . . 1251(96)
p53
tumor suppressor p53


M00253
135 . . . 142(96)
cap
cap signal for transcription initiation



457 . . . 464(95)



1871 . . . 1864(95)



721 . . . 728(94)



1461 . . . 1454(92)



312 . . . 319(92)



1989 . . . 1996(92)



1855 . . . 1848(91)



770 . . . 777(90)



1793 . . . 1786(90)



295 . . . 302(90)



1274 . . . 1281(90)


M00106
627 . . . 636(95)
CDP
cut-like homeodomain protein



634 . . . 625(93)


M00116
1215 . . . 1202(95)
C/EBPalpha
CCAAT/enhancer binding protein alpha


M00254
1809 . . . 1798(95)
CCAAT
cellular and viral CCAAT box


M00249
1117 . . . 1105(95)
CHOP-
heterodimers of CHOP and C/EBPalpha




C/EBPalpha


M00054
442 . . . 433(95)
NF-kappaB
NF-kappaB


M00147
2182 . . . 2173(94)
HSF2
heat shock factor 2



2173 . . . 2182(92)



754 . . . 745(91)



141 . . . 132(90)


M00104
634 . . . 625(94)
CDP
cut-like homeodomain protein



2 . . . 11(92)


M00134
280 . . . 298(94)
HNF-4
hepatic nuclear factor 4


M00052
442 . . . 433(94)
NF-kappaB
NF-kappaB (p65)


M00053
442 . . . 433(94)
c-Rel
c-Rel



785 . . . 794(90)


M00033
731 . . . 718(94)
p300
p300


M00158
295 . . . 282(93)
COUP-TF
COUP/HNF-4 heterodimer


M00032
225 . . . 216(93)
c-Ets-1(p54)
c-Ets-1(p54)



226 . . . 235(93)


M00172
1851 . . . 1861(92)
AP-1
activator protein 1


M00223
520 . . . 512(92)
STATx
signal transducers and activators of transcription


M00075
1679 . . . 1670(92)
GATA-1
GATA-binding factor 1



1867 . . . 1876(91)



716 . . . 707(91)



316 . . . 307(90)


M00184
1463 . . . 1472(91)
MyoD
myoblast determining factor



1472 . . . 1463(91)



247 . . . 256(90)



2057 . . . 2048(90)


M00289
357 . . . 369(91)
HFH-3
HNF-3/Fkh Homolog 3 (= Freac-6)


M00109
1202 . . . 1215(91)
C/EBPbeta
CCAAT/enhancer binding protein beta



2036 . . . 2023(90)


M00268
937 . . . 950(91)
XFD-2
Xenopus fork head domain factor 2


M00208
443 . . . 432(90)
NF-kappaB
NF-kappaB binding site


M00173
1851 . . . 1861(90)
AP-1
activator protein 1


M00183
1002 . . . 1011(90)
c-Myb
c-Myb



2020 . . . 2011(90)


M00240
217 . . . 211(90)
Nkx-2.5.
homeo domain factor Nkx-2.5/Csx, tinman homolog


M00188
1851 . . . 1861(90)
AP-1
activator protein 1


M00099
1086 . . . 1101(90)
S8
S8


M00302
813 . . . 802(90)
NF-AT
Nuclear factor of activated T-cells


M00083
21 . . . 14(90)
MZF1
MZF1


M00190
1215 . . . 1202(90)
C/EBP
CCAAT/enhancer binding factor


M00221
1838 . . . 1828(90)
SREBP-1
sterol regulatory element-binding protein 1


M00294
949 . . . 937(90)
HFH-8
HNF-3/Fkh Homolog-8


M00137
1365 . . . 1353(90)
Oct-1
octamer factor 1


M00077
1911 . . . 1919(90)
GATA-3
GATA-binding factor 3


M00194
444 . . . 431(90)
NF-kappaB
NF-kappaB
















TABLE 9







putative transcription factor binding motifs within the DUB regulatory or promoter,


region of hDUB 4.2b. The position is indicated by nucleotides.










Transfac
Position(Score)
Name
Description





M00100
1102 . . . 1096(100)
CdxA
CdxA


M00148
1017 . . . 1011(100)
SRY
sex-determining region Y gene product



967 . . . 973(100)



944 . . . 938(96)



1566 . . . 1572(92)



1530 . . . 1536(92)



840 . . . 834(90)



1093 . . . 1099(90)



705 . . . 711(90)



1362 . . . 1356(90)



1719 . . . 1713(90)



1824 . . . 1818(90)



393 . . . 387(90)



746 . . . 740(90)



299 . . . 305(90)


M00253
1120 . . . 1127(99)
cap
cap signal for transcription initiation



160 . . . 167(96)



482 . . . 489(95)



1893 . . . 1886(95)



746 . . . 753(94)



1486 . . . 1479(92)



337 . . . 344(92)



1877 . . . 1870(91)



795 . . . 802(90)



1815 . . . 1808(90)



320 . . . 327(90)



1299 . . . 1306(90)


M00101
1102 . . . 1096(99)
CdxA
CdxA



830 . . . 824(98)



1231 . . . 1225(98)



1409 . . . 1415(92)



724 . . . 718(92)



520 . . . 526(92)



1682 . . . 1688(91)



1688 . . . 1682(91)


M00076
741 . . . 732(98)
GATA-2
GATA-binding factor 2



1932 . . . 1941(95)



984 . . . 993(92)



1701 . . . 1692(91)


M00285
1734 . . . 1746(96)
TCF11
TCF11/KCR-F1/Nrf1 homodimers



1112 . . . 1124(91)


M00272
1267 . . . 1276(96)
p53
tumor suppressor p53


M00106
652 . . . 661(95)
CDP
cut-like homeodomain protein



659 . . . 650(93)


M00116
1240 . . . 1227(95)
C/EBPalpha
CCAAT/enhancer binding protein alpha


M00254
1831 . . . 1820(95)
CCAAT
cellular and viral CCAAT box


M00249
1142 . . . 1130(95)
CHOP-
heterodimers of CHOP and C/EBPalpha




C/EBPalpha


M00054
467 . . . 458(95)
NF-kappaB
NF-kappaB


M00104
659 . . . 650(94)
CDP
cut-like homeodomain protein



27 . . . 36(92)


M00134
305 . . . 323(94)
HNF-4
hepatic nuclear factor 4


M00052
467 . . . 458(94)
NF-kappaB
NF-kappaB (p65)


M00053
467 . . . 458(94)
c-Rel
c-Rel


M00033
756 . . . 743(94)
p300
p300


M00158
320 . . . 307(93)
COUP-TF
COUP/HNF-4 heterodimer


M00075
1889 . . . 1898(93)
GATA-1
GATA-binding factor 1



1701 . . . 1692(92)



741 . . . 732(91)



341 . . . 332(90)



641 . . . 632(90)


M00160
965 . . . 976(93)
SRY
sex-determining region Y gene product


M00032
250 . . . 241(93)
c-Ets-
c-Ets-1(p54)



251 . . . 260(93)
1(p54)


M00172
1873 . . . 1883(92)
AP-1
activator protein 1


M00223
545 . . . 537(92)
STATx
signal transducers and activators of transcription


M00271
1955 . . . 1960(92)
AML-1a
runt-factor AML-1


M00184
1488 . . . 1497(91)
MyoD
myoblast determining factor



1497 . . . 1488(91)



272 . . . 281(90)


M00289
382 . . . 394(91)
HFH-3
HNF-3/Fkh Homolog 3 (= Freac-6)


M00109
1227 . . . 1240(91)
C/EBPbeta
CCAAT/enhancer binding protein beta


M00147
779 . . . 770(91)
HSF2
heat shock factor 2



166 . . . 157(90)


M00208
468 . . . 457(90)
NF-kappaB
NF-kappaB binding site


M00183
1027 . . . 1036(90)
c-Myb
c-Myb


M00173
1873 . . . 1883(90)
AP-1
activator protein 1


M00240
242 . . . 236(90)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman





homolog


M00188
1873 . . . 1883(90)
AP-1
activator protein 1


M00302
838 . . . 827(90)
NF-AT
Nuclear factor of activated T-cells


M00083
46 . . . 39(90)
MZF1
MZF1


M00190
1240 . . . 1227(90)
C/EBP
CCAAT/enhancer binding factor


M00096
1115 . . . 1123(90)
Pbx-1
Pbx-1


M00221
1860 . . . 1850(90)
SREBP-1
sterol regulatory element-binding protein 1


M00194
469 . . . 456(90)
NF-kappaB
NF-kappaB


M00077
1933 . . . 1941(90)
GATA-3
GATA-binding factor 3
















TABLE 10







putative transcription factor binding motifs within the DUB regulatory or promoter,


region of hDUB 4.3. The position is indicated by nucleotides.










Transfac
Position(Score)
Name
Description





M00148
1015 . . . 1009(100)
SRY
sex-determining region Y gene product



965 . . . 971(100)



942 . . . 936(96)



1566 . . . 1572(92)



1528 . . . 1534(92)



838 . . . 832(90)



1091 . . . 1097(90)



1219 . . . 1213(90)



703 . . . 709(90)



1360 . . . 1354(90)



1719 . . . 1713(90)



1824 . . . 1818(90)



391 . . . 385(90)



744 . . . 738(90)



297 . . . 303(90)


M00100
1100 . . . 1094(100)
CdxA
CdxA


M00101
1100 . . . 1094(99)
CdxA
CdxA



828 . . . 822(98)



1407 . . . 1413(92)



722 . . . 716(92)



959 . . . 965(92)



518 . . . 524(92)



1682 . . . 1688(91)



1688 . . . 1682(91)


M00076
739 . . . 730(98)
GATA-2
GATA-binding factor 2



1932 . . . 1941(95)



982 . . . 991(92)



1701 . . . 1692(91)


M00285
1734 . . . 1746(96)
TCF11
TCF11/KCR-F1/Nrf1 homodimers



1110 . . . 1122(91)


M00272
1265 . . . 1274(96)
p53
tumor suppressor p53


M00253
158 . . . 165(96)
cap
cap signal for transcription initiation



480 . . . 487(95)



1893 . . . 1886(95)



744 . . . 751(94)



1484 . . . 1477(92)



335 . . . 342(92)



1877 . . . 1870(91)



793 . . . 800(90)



318 . . . 325(90)



1297 . . . 1304(90)


M00106
650 . . . 659(95)
CDP
cut-like homeodomain protein



657 . . . 648(93)


M00116
1238 . . . 1225(95)
C/EBPalpha
CCAAT/enhancer binding protein alpha


M00254
1831 . . . 1820(95)
CCAAT
cellular and viral CCAAT box


M00249
1140 . . . 1128(95)
CHOP-
heterodimers of CHOP and C/EBPalpha




C/EBPalpha


M00054
465 . . . 456(95)
NF-kappaB
NF-kappaB


M00104
657 . . . 648(94)
CDP
cut-like homeodomain protein



25 . . . 34(92)


M00134
303 . . . 321(94)
HNF-4
hepatic nuclear factor 4


M00052
465 . . . 456(94)
NF-kappaB
NF-kappaB (p65)


M00053
465 . . . 456(94)
c-Rel
c-Rel


M00033
754 . . . 741(94)
p300
p300


M00158
318 . . . 305(93)
COUP-TF
COUP/HNF-4 heterodimer


M00075
1889 . . . 1898(93)
GATA-1
GATA-binding factor 1



1701 . . . 1692(92)



739 . . . 730(91)



339 . . . 330(90)


M00160
963 . . . 974(93)
SRY
sex-determining region Y gene product


M00032
248 . . . 239(93)
c-Ets-
c-Ets-1(p54)



249 . . . 258(93)
1(p54)


M00172
1873 . . . 1883(92)
AP-1
activator protein 1


M00223
543 . . . 535(92)
STATx
signal transducers and activators of transcription


M00271
1955 . . . 1960(92)
AML-1a
runt-factor AML-1


M00173
1873 . . . 1883(91)
AP-1
activator protein 1


M00184
1486 . . . 1495(91)
MyoD
myoblast determining factor



1495 . . . 1486(91)



270 . . . 279(90)


M00289
380 . . . 392(91)
HFH-3
HNF-3/Fkh Homolog 3 (= Freac-6)


M00109
1225 . . . 1238(91)
C/EBPbeta
CCAAT/enhancer binding protein beta


M00147
777 . . . 768(91)
HSF2
heat shock factor 2



164 . . . 155(90)


M00208
466 . . . 455(90)
NF-kappaB
NF-kappaB binding site


M00183
1025 . . . 1034(90)
c-Myb
c-Myb


M00240
240 . . . 234(90)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman





homolog


M00099
1109 . . . 1124(90)
S8
S8


M00302
836 . . . 825(90)
NF-AT
Nuclear factor of activated T-cells


M00083
44 . . . 37(90)
MZF1
MZF1


M00190
1238 . . . 1225(90)
C/EBP
CCAAT/enhancer binding factor


M00221
1860 . . . 1850(90)
SREBP-1
sterol regulatory element-binding protein 1


M00174
1873 . . . 1883(90)
AP-1
activator protein 1


M00077
1933 . . . 1941(90)
GATA-3
GATA-binding factor 3


M00194
467 . . . 454(90)
NF-kappaB
NF-kappaB
















TABLE 11







putative transcription factor binding motifs within the DUB regulatory or promoter,


region of hDUB 4.4. The position is indicated by nucleotides.










Transfac
Position(Score)
Name
Description





M00100
1101 . . . 1095(100)
CdxA
CdxA


M00148
1016 . . . 1010(100)
SRY
sex-determining region Y gene product



966 . . . 972(100)



944 . . . 938(96)



1566 . . . 1572(92)



1529 . . . 1535(92)



840 . . . 834(90)



1092 . . . 1098(90)



705 . . . 711(90)



1361 . . . 1355(90)



1719 . . . 1713(90)



1824 . . . 1818(90)



393 . . . 387(90)



746 . . . 740(90)



299 . . . 305(90)


M00101
1101 . . . 1095(99)
CdxA
CdxA



830 . . . 824(98)



1230 . . . 1224(98)



1408 . . . 1414(92)



724 . . . 718(92)



520 . . . 526(92)



1682 . . . 1688(91)



1688 . . . 1682(91)


M00076
741 . . . 732(98)
GATA-2
GATA-binding factor 2



1932 . . . 1941(95)



983 . . . 992(92)



1701 . . . 1692(91)


M00350
876 . . . 867(96)
GATA-3
GATA-binding factor 3


M00285
1734 . . . 1746(96)
TCF11
TCF11/KCR-F1/Nrf1 homodimers



1111 . . . 1123(91)


M00272
1266 . . . 1275(96)
p53
tumor suppressor p53


M00253
160 . . . 167(96)
cap
cap signal for transcription initiation



482 . . . 489(95)



1893 . . . 1886(95)



746 . . . 753(94)



1485 . . . 1478(92)



337 . . . 344(92)



1877 . . . 1870(91)



795 . . . 802(90)



1815 . . . 1808(90)



320 . . . 327(90)



1298 . . . 1305(90)


M00106
652 . . . 661(95)
CDP
cut-like homeodomain protein



659 . . . 650(93)


M00116
1239 . . . 1226(95)
C/EBPalpha
CCAAT/enhancer binding protein alpha


M00254
1831 . . . 1820(95)
CCAAT
cellular and viral CCAAT box


M00249
1141 . . . 1129(95)
CHOP-
heterodimers of CHOP and C/EBPalpha




C/EBPalpha


M00349
876 . . . 867(95)
GATA-2
GATA-binding factor 2


M00054
467 . . . 458(95)
NF-kappaB
NF-kappaB


M00104
659 . . . 650(94)
CDP
cut-like homeodomain protein



27 . . . 36(92)


M00134
305 . . . 323(94)
HNF-4
hepatic nuclear factor 4


M00052
467 . . . 458(94)
NF-kappaB
NF-kappaB (p65)


M00053
467 . . . 458(94)
c-Rel
c-Rel


M00033
756 . . . 743(94)
p300
p300


M00348
876 . . . 867(93)
GATA-2
GATA-binding factor 2


M00158
320 . . . 307(93)
COUP-TF
COUP/HNF-4 heterodimer


M00075
1889 . . . 1898(93)
GATA-1
GATA-binding factor 1



1701 . . . 1692(92)



741 . . . 732(91)



341 . . . 332(90)


M00160
964 . . . 975(93)
SRY
sex-determining region Y gene product


M00347
876 . . . 867(93)
GATA-1
GATA-binding factor 1


M00032
250 . . . 241(93)
c-Ets-1(p54)
c-Ets-1(p54)



251 . . . 260(93)


M00172
1873 . . . 1883(92)
AP-1
activator protein 1


M00223
545 . . . 537(92)
STATx
signal transducers and activators of transcription


M00271
1955 . . . 1960(92)
AML-1a
runt-factor AML-1


M00184
1487 . . . 1496(91)
MyoD
myoblast determining factor



1496 . . . 1487(91)



272 . . . 281(90)


M00289
382 . . . 394(91)
HFH-3
HNF-3/Fkh Homolog 3 (= Freac-6)


M00109
1226 . . . 1239(91)
C/EBPbeta
CCAAT/enhancer binding protein beta


M00208
468 . . . 457(90)
NF-kappaB
NF-kappaB binding site


M00183
1026 . . . 1035(90)
c-Myb
c-Myb


M00173
1873 . . . 1883(90)
AP-1
activator protein 1


M00240
242 . . . 236(90)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman





homolog


M00188
1873 . . . 1883(90)
AP-1
activator protein 1


M00099
1110 . . . 1125(90)
S8
S8


M00302
838 . . . 827(90)
NF-AT
Nuclear factor of activated T-cells


M00083
46 . . . 39(90)
MZF1
MZF1


M00190
1239 . . . 1226(90)
C/EBP
CCAAT/enhancer binding factor


M00147
166 . . . 157(90)
HSF2
heat shock factor 2


M00080
874 . . . 864(90)
Evi-1
ectopic viral integration site 1 encoded factor


M00082
874 . . . 864(90)
Evi-1
ectopic viral integration site 1 encoded factor


M00221
1860 . . . 1850(90)
SREBP-1
sterol regulatory element-binding protein 1


M00194
469 . . . 456(90)
NF-kappaB
NF-kappaB


M00077
1933 . . . 1941(90)
GATA-3
GATA-binding factor 3
















TABLE 12







putative transcription factor binding motifs within the DUB regulatory or promoter,


region of hDUB 4.5. The position is indicated by nucleotides.










Transfac
Position(Score)
Name
Description





M00148
963 . . . 969(100)
SRY
sex-determining region Y gene product



1013 . . . 1007(100)



940 . . . 934(96)



1526 . . . 1532(92)



1089 . . . 1095(90)



836 . . . 830(90)



701 . . . 707(90)



1358 . . . 1352(90)



1720 . . . 1714(90)



1825 . . . 1819(90)



389 . . . 383(90)



742 . . . 736(90)



295 . . . 301(90)


M00100
1098 . . . 1092(100)
CdxA
CdxA


M00101
1098 . . . 1092(99)
CdxA
CdxA



826 . . . 820(98)



1405 . . . 1411(92)



720 . . . 714(92)



957 . . . 963(92)



516 . . . 522(92)



1683 . . . 1689(91)



1689 . . . 1683(91)


M00076
737 . . . 728(98)
GATA-2
GATA-binding factor 2



980 . . . 989(92)



1702 . . . 1693(91)



1299 . . . 1308(90)


M00285
1735 . . . 1747(96)
TCF11
TCF11/KCR-F1/Nrf1 homodimers



1108 . . . 1120(91)


M00272
1263 . . . 1272(96)
p53
tumor suppressor p53


M00253
156 . . . 163(96)
cap
cap signal for transcription initiation



478 . . . 485(95)



742 . . . 749(94)



1482 . . . 1475(92)



333 . . . 340(92)



791 . . . 798(90)



1816 . . . 1809(90)



316 . . . 323(90)


M00106
648 . . . 657(95)
CDP
cut-like homeodomain protein



655 . . . 646(93)


M00116
1236 . . . 1223(95)
C/EBPalpha
CCAAT/enhancer binding protein alpha


M00254
1832 . . . 1821(95)
CCAAT
cellular and viral CCAAT box


M00249
1138 . . . 1126(95)
CHOP-
heterodimers of CHOP and C/EBPalpha




C/EBPalpha


M00054
463 . . . 454(95)
NF-kappaB
NF-kappaB


M00183
1493 . . . 1484(94)
c-Myb
c-Myb



1023 . . . 1032(90)


M00104
655 . . . 646(94)
CDP
cut-like homeodomain protein



23 . . . 32(92)


M00134
301 . . . 319(94)
HNF-4
hepatic nuclear factor 4


M00052
463 . . . 454(94)
NF-kappaB
NF-kappaB (p65)


M00053
463 . . . 454(94)
c-Rel
c-Rel



806 . . . 815(90)


M00033
752 . . . 739(94)
p300
p300


M00158
316 . . . 303(93)
COUP-TF
COUP/HNF-4 heterodimer


M00032
246 . . . 237(93)
c-Ets-
c-Ets-1(p54)



247 . . . 256(93)
1(p54)


M00278
1300 . . . 1308(92)
Lmo2
complex of Lmo2 bound to Tal-1, E2A proteins, and





GATA-1, half-site 2


M00223
541 . . . 533(92)
STATx
signal transducers and activators of transcription


M00075
1702 . . . 1693(92)
GATA-1
GATA-binding factor 1



737 . . . 728(91)



337 . . . 328(90)


M00077
1300 . . . 1308(91)
GATA-3
GATA-binding factor 3


M00289
378 . . . 390(91)
HFH-3
HNF-3/Fkh Homolog 3 (= Freac-6)


M00109
1223 . . . 1236(91)
C/EBPbeta
CCAAT/enhancer binding protein beta


M00268
958 . . . 971(91)
XFD-2
Xenopus fork head domain factor 2


M00147
775 . . . 766(91)
HSF2
heat shock factor 2



162 . . . 153(90)


M00208
464 . . . 453(90)
NF-kappaB
NF-kappaB binding site


M00240
238 . . . 232(90)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog


M00099
1107 . . . 1122(90)
S8
S8


M00302
834 . . . 823(90)
NF-AT
Nuclear factor of activated T-cells


M00083
42 . . . 35(90)
MZF1
MZF1


M00184
268 . . . 277(90)
MyoD
myoblast determining factor


M00190
1236 . . . 1223(90)
C/EBP
CCAAT/enhancer binding factor


M00221
1861 . . . 1851(90)
SREBP-1
sterol regulatory element-binding protein 1


M00294
970 . . . 958(90)
HFH-8
HNF-3/Fkh Homolog-8


M00137
1386 . . . 1374(90)
Oct-1
octamer factor 1


M00194
465 . . . 452(90)
NF-kappaB
NF-kappaB
















TABLE 13







putative transcription factor binding motifs within the DUB regulatory or promoter,


region of hDUB 8.1. The position is indicated by nucleotides.










Transfac
Position(Score)
Name
Description





M00148
1015 . . . 1009(100)
SRY
sex-determining region Y gene product



965 . . . 971(100)



942 . . . 936(96)



1544 . . . 1550(92)



838 . . . 832(90)



702 . . . 708(90)



1719 . . . 1713(90)



1824 . . . 1818(90)



390 . . . 384(90)



1384 . . . 1390(90)



1356 . . . 1350(90)



296 . . . 302(90)



63 . . . 69(90)


M00100
1100 . . . 1094(100)
CdxA
CdxA



724 . . . 730(96)



1547 . . . 1541(91)


M00349
93 . . . 102(100)
GATA-2
GATA-binding factor 2


M00350
93 . . . 102(100)
GATA-3
GATA-binding factor 3


M00241
1800 . . . 1807(100)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog


M00348
93 . . . 102(100)
GATA-2
GATA-binding factor 2


M00101
1100 . . . 1094(99)
CdxA
CdxA



828 . . . 822(98)



1229 . . . 1223(98)



1203 . . . 1209(94)



721 . . . 715(92)



959 . . . 965(92)



1386 . . . 1380(92)



65 . . . 59(92)



517 . . . 523(92)



419 . . . 425(92)



1682 . . . 1688(91)



1688 . . . 1682(91)


M00203
95 . . . 105(98)
GATA-X
GATA binding site


M00347
93 . . . 102(97)
GATA-1
GATA-binding factor 1


M00075
1838 . . . 1847(97)
GATA-1
GATA-binding factor 1



1701 . . . 1692(95)



137 . . . 128(92)



1483 . . . 1492(92)



1889 . . . 1898(91)



1736 . . . 1745(90)


M00158
317 . . . 304(96)
COUP-
COUP/HNF-4 heterodimer




TF


M00253
158 . . . 165(96)
cap
cap signal for transcription initiation



1794 . . . 1801(95)



479 . . . 486(95)



1297 . . . 1304(93)



337 . . . 344(93)



48 . . . 55(93)



1484 . . . 1477(92)



1324 . . . 1317(91)



557 . . . 564(91)



1893 . . . 1886(91)



1877 . . . 1870(91)



793 . . . 800(90)



1356 . . . 1363(90)



1815 . . . 1808(90)



317 . . . 324(90)


M00285
1734 . . . 1746(95)
TCF11
TCF11/KCR-F1/Nrf1 homodimers



1110 . . . 1122(91)



13 . . . 1(90)


M00134
302 . . . 320(95)
HNF-4
hepatic nuclear factor 4


M00077
1933 . . . 1941(95)
GATA-3
GATA-binding factor 3


M00096
1827 . . . 1819(95)
Pbx-1
Pbx-1


M00141
451 . . . 459(94)
Lyf-1
LyF-1


M00199
1797 . . . 1789(94)
AP-1
AP-1 binding site



1789 . . . 1797(91)


M00174
1788 . . . 1798(94)
AP-1
activator protein 1


M00076
1483 . . . 1492(93)
GATA-2
GATA-binding factor 2



1932 . . . 1941(93)



1701 . . . 1692(92)



982 . . . 991(92)


M00278
1933 . . . 1941(93)
Lmo2
complex of Lmo2 bound to Tal-1, E2A proteins, and





GATA-1, half-site 2


M00099
1813 . . . 1798(92)
S8
S8



1109 . . . 1124(90)


M00294
1551 . . . 1539(92)
HFH-8
HNF-3/Fkh Homolog-8


M00223
542 . . . 534(92)
STATx
signal transducers and activators of transcription


M00073
36 . . . 46(92)
deltaEF1
deltaEF1


M00271
1955 . . . 1960(92)
AML-1a
runt-factor AML-1



132 . . . 127(92)


M00137
335 . . . 323(91)
Oct-1
octamer factor 1


M00042
644 . . . 653(91)
Sox-5
Sox-5



1829 . . . 1820(90)


M00289
379 . . . 391(91)
HFH-3
HNF-3/Fkh Homolog 3 (= Freac-6)


M00183
1025 . . . 1034(90)
c-Myb
c-Myb


M00240
239 . . . 233(90)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog


M00188
1788 . . . 1798(90)
AP-1
activator protein 1


M00302
836 . . . 825(90)
NF-AT
Nuclear factor of activated T-cells


M00128
92 . . . 104(90)
GATA-1
GATA-binding factor 1


M00184
269 . . . 278(90)
MyoD
myoblast determining factor


M00147
164 . . . 155(90)
HSF2
heat shock factor 2


M00087
979 . . . 990(90)
Ik-2
Ikaros 2


M00172
1788 . . . 1798(90)
AP-1
activator protein 1


M00221
1860 . . . 1850(90)
SREBP-1
sterol regulatory element-binding protein 1
















TABLE 14







putative transcription factor binding motifs within the DUB regulatory or promoter,


region of hDUB 8.2. The position is indicated by nucleotides.










Transfac
Position(Score)
Name
Description





M00241
1804 . . . 1811(100)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog


M00240
556 . . . 562(100)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog



1354 . . . 1360(90)



301 . . . 307(90)


M00096
1342 . . . 1350(100)
Pbx-1
Pbx-1



1831 . . . 1823(96)


M00271
702 . . . 707(100)
AML-1a
runt-factor AML-1



1955 . . . 1960(92)



170 . . . 175(92)


M00050
104 . . . 111(100)
E2F
E2F


M00148
1271 . . . 1277(100)
SRY
sex-determining region Y gene product



1572 . . . 1578(92)



1345 . . . 1351(90)



1719 . . . 1713(90)



1828 . . . 1822(90)



1634 . . . 1628(90)


M00272
472 . . . 463(97)
p53
tumor suppressor p53



463 . . . 472(97)



295 . . . 286(91)


M00075
1842 . . . 1851(97)
GATA-1
GATA-binding factor 1



1893 . . . 1902(93)



1380 . . . 1371(92)



1740 . . . 1749(90)


M00253
1072 . . . 1065(96)
cap
cap signal for transcription initiation



1798 . . . 1805(95)



1897 . . . 1890(95)



769 . . . 776(92)



1701 . . . 1708(92)



1881 . . . 1874(91)



497 . . . 504(90)



1819 . . . 1812(90)



21 . . . 28(90)


M00285
1738 . . . 1750(95)
TCF11
TCF11/KCR-F1/Nrf1 homodimers



366 . . . 378(93)


M00077
1933 . . . 1941(95)
GATA-3
GATA-binding factor 3


M00147
148 . . . 139(94)
HSF2
heat shock factor 2



139 . . . 148(92)


M00199
1801 . . . 1793(94)
AP-1
AP-1 binding site



1037 . . . 1029(94)



1793 . . . 1801(91)



1029 . . . 1037(90)


M00174
1792 . . . 1802(94)
AP-1
activator protein 1



1038 . . . 1028(92)


M00074
1247 . . . 1259(93)
c-Ets-
c-Ets-1(p54)




1(p54)


M00211
702 . . . 710(93)
Poly
Retroviral Poly A downstream element



1531 . . . 1539(91)


M00124
1339 . . . 1353(93)
Pbx1b
homeo domain factor Pbx-1


M00278
1933 . . . 1941(93)
Lmo2
complex of Lmo2 bound to Tal-1, E2A proteins, and





GATA-1, half-site 2


M00052
1261 . . . 1252(93)
NF-
NF-kappaB (p65)




kappaB


M00076
1932 . . . 1941(93)
GATA-2
GATA-binding factor 2



837 . . . 828(90)


M00099
1817 . . . 1802(92)
S8
S8


M00101
987 . . . 981(92)
CdxA
CdxA


M00042
1635 . . . 1626(92)
Sox-5
Sox-5


M00254
1835 . . . 1824(91)
CCAAT
cellular and viral CCAAT box


M00008
252 . . . 243(91)
Sp1
stimulating protein 1



1323 . . . 1314(91)


M00227
933 . . . 941(90)
v-Myb
v-Myb


M00141
1328 . . . 1320(90)
Lyf-1
LyF-1


M00183
1033 . . . 1042(90)
c-Myb
c-Myb


M00001
654 . . . 665(90)
MyoD
myoblast determination gene product


M00188
1792 . . . 1802(90)
AP-1
activator protein 1


M00184
23 . . . 14(90)
MyoD
myoblast determining factor


M00172
1792 . . . 1802(90)
AP-1
activator protein 1


M00221
1864 . . . 1854(90)
SREBP-1
sterol regulatory element-binding protein 1


M00037
871 . . . 861(90)
NF-E2
NF-E2 p45


M00053
1261 . . . 1252(90)
c-Rel
c-Rel


M00249
823 . . . 835(90)
CHOP-
heterodimers of CHOP and C/EBPalpha




C/EBPalpha


M00302
1248 . . . 1259(90)
NF-AT
Nuclear factor of activated T-cells
















TABLE 15







putative transcription factor binding motifs within the DUB regulatory or promoter,


region of hDUB 8.3. The position is indicated by nucleotides.










Transfac
Position(Score)
Name
Description





M00348
71 . . . 80(100)
GATA-2
GATA-binding factor 2


M00349
71 . . . 80(100)
GATA-2
GATA-binding factor 2


M00148
990 . . . 984(100)
SRY
sex-determining region Y gene product



1654 . . . 1648(100)



813 . . . 807(96)



917 . . . 911(96)



1848 . . . 1854(92)



1840 . . . 1846(92)



1826 . . . 1832(92)



1504 . . . 1498(92)



1391 . . . 1397(90)



680 . . . 686(90)



2094 . . . 2088(90)



368 . . . 362(90)



721 . . . 715(90)



1002 . . . 996(90)



1900 . . . 1894(90)



274 . . . 280(90)


M00350
71 . . . 80(100)
GATA-3
GATA-binding factor 3


M00100
595 . . . 589(100)
CdxA
CdxA



1400 . . . 1394(100)


M00101
595 . . . 589(99)
CdxA
CdxA



1400 . . . 1394(99)



803 . . . 797(98)



1527 . . . 1521(98)



1705 . . . 1711(92)



699 . . . 693(92)



934 . . . 940(92)



43 . . . 37(92)



495 . . . 501(92)



397 . . . 403(92)


M00141
1274 . . . 1266(98)
Lyf-1
LyF-1


M00347
71 . . . 80(97)
GATA- 1
GATA-binding factor 1


M00272
1563 . . . 1572(96)
p53
tumor suppressor p53


M00253
1128 . . . 1135(96)
cap
cap signal for transcription initiation



136 . . . 143(96)



2064 . . . 2071(95)



457 . . . 464(95)



2163 . . . 2156(95)



721 . . . 728(94)



660 . . . 653(94)



1782 . . . 1775(92)



312 . . . 319(92)



1622 . . . 1615(91)



535 . . . 542(91)



2085 . . . 2078(91)



2147 . . . 2140(91)



1350 . . . 1357(91)



768 . . . 775(90)



295 . . . 302(90)


M00285
2004 . . . 2016(95)
TCF11
TCF11/KCR-F1/Nrf1 homodimers



1410 . . . 1422(91)


M00254
2101 . . . 2090(95)
CCAAT
cellular and viral CCAAT box


M00130
1647 . . . 1658(95)
HFH-2
HNF-3/Fkh Homolog 2


M00054
442 . . . 433(95)
NF-kappaB
NF-kappaB


M00077
2203 . . . 2211(95)
GATA-3
GATA-binding factor 3


M00052
442 . . . 433(94)
NF-kappaB
NF-kappaB (p65)


M00203
73 . . . 83(94)
GATA-X
GATA binding site


M00199
2067 . . . 2059(94)
AP-1
AP-1 binding site



2059 . . . 2067(91)



1984 . . . 1992(90)


M00174
2058 . . . 2068(94)
AP-1
activator protein 1


M00075
895 . . . 886(94)
GATA-1
GATA-binding factor 1



2159 . . . 2168(93)



1082 . . . 1073(93)



1971 . . . 1962(92)



2006 . . . 2015(90)


M00053
442 . . . 433(94)
c-Rel
c-Rel


M00241
2070 . . . 2077(94)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog


M00076
716 . . . 707(94)
GATA-2
GATA-binding factor 2



1599 . . . 1608(92)



957 . . . 966(92)



895 . . . 886(91)



1971 . . . 1962(91)


M00106
627 . . . 636(94)
CDP
cut-like homeodomain protein


M00033
731 . . . 718(94)
p300
p300


M00227
2139 . . . 2131(94)
v-Myb
v-Myb


M00158
295 . . . 282(93)
COUP-TF
COUP/HNF-4 heterodimer


M00162
2070 . . . 2083(93)
Oct-1
octamer-binding factor 1


M00134
280 . . . 298(93)
HNF-4
hepatic nuclear factor 4


M00032
226 . . . 235(93)
c-Ets-1(p54)
c-Ets-1(p54)


M00117
1080 . . . 1067(92)
C/EBPbeta
CCAAT/enhancer binding protein beta


M00223
520 . . . 512(92)
STATx
signal transducers and activators of transcription


M00042
1901 . . . 1892(92)
Sox-5
Sox-5



622 . . . 631(91)


M00073
13 . . . 23(92)
deltaEF1
deltaEF1


M00099
2083 . . . 2068(91)
S8
S8



2066 . . . 2081(90)



1409 . . . 1424(90)


M00289
1647 . . . 1659(91)
HFH-3
HNF-3/Fkh Homolog 3 (= Freac-6)



357 . . . 369(91)


M00147
752 . . . 743(91)
HSF2
heat shock factor 2



142 . . . 133(90)


M00208
443 . . . 432(90)
NF-kappaB
NF-kappaB binding site


M00217
115 . . . 108(90)
USF
USF binding site


M00183
1325 . . . 1334(90)
c-Myb
c-Myb


M00240
217 . . . 211(90)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog


M00188
2058 . . . 2068(90)
AP-1
activator protein 1


M00184
1955 . . . 1964(90)
MyoD
myoblast determining factor



247 . . . 256(90)


M00087
954 . . . 965(90)
Ik-2
Ikaros 2


M00128
70 . . . 82(90)
GATA-1
GATA-binding factor 1


M00172
2058 . . . 2068(90)
AP-1
activator protein 1


M00145
1339 . . . 1354(90)
Brn-2
POU factor Brn-2


M00062
1217 . . . 1205(90)
IRF-1
interferon regulatory factor 1


M00194
444 . . . 431(90)
NF-kappaB
NF-kappaB
















TABLE 16







putative transcription factor binding motifs within the DUB regulatory or promoter,


region of hDUB 8.4. The position is indicated by nucleotides.










Transfac
Position(Score)
Name
Description





M00100
1105 . . . 1099(100)
CdxA
CdxA


M00241
1800 . . . 1807(100)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog


M00148
1020 . . . 1014(100)
SRY
sex-determining region Y gene product



970 . . . 976(100)



947 . . . 941(96)



1550 . . . 1556(92)



843 . . . 837(90)



707 . . . 713(90)



1362 . . . 1356(90)



1719 . . . 1713(90)



1824 . . . 1818(90)



395 . . . 389(90)



748 . . . 742(90)



300 . . . 306(90)


M00101
1105 . . . 1099(99)
CdxA
CdxA



833 . . . 827(98)



1385 . . . 1379(98)



1409 . . . 1415(92)



964 . . . 970(92)



726 . . . 720(92)



424 . . . 430(92)


M00075
1838 . . . 1847(97)
GATA-1
GATA-binding factor 1



1889 . . . 1898(93)



925 . . . 916(93)



1736 . . . 1745(90)


M00272
1267 . . . 1276(96)
p53
tumor suppressor p53


M00253
161 . . . 168(96)
cap
cap signal for transcription initiation



1794 . . . 1801(95)



484 . . . 491(95)



1893 . . . 1886(95)



1452 . . . 1459(94)



798 . . . 805(94)



748 . . . 755(94)



957 . . . 964(94)



1486 . . . 1479(92)



338 . . . 345(92)



1697 . . . 1704(92)



562 . . . 569(91)



1877 . . . 1870(91)



1815 . . . 1808(90)



321 . . . 328(90)



1326 . . . 1319(90)



1299 . . . 1306(90)


M00096
1827 . . . 1819(96)
Pbx-1
Pbx-1


M00285
1734 . . . 1746(95)
TCF11
TCF11/KCR-F1/Nrf1 homodimers



1115 . . . 1127(91)


M00077
1933 . . . 1941(95)
GATA-3
GATA-binding factor 3


M00054
469 . . . 460(95)
NF-kappaB
NF-kappaB


M00141
456 . . . 464(94)
Lyf-1
LyF-1


M00134
306 . . . 324(94)
HNF-4
hepatic nuclear factor 4


M00052
469 . . . 460(94)
NF-kappaB
NF-kappaB (p65)


M00199
1797 . . . 1789(94)
AP-1
AP-1 binding site



1789 . . . 1797(91)


M00174
1788 . . . 1798(94)
AP-1
activator protein 1


M00053
469 . . . 460(94)
c-Rel
c-Rel


M00033
758 . . . 745(94)
p300
p300



808 . . . 795(92)


M00158
321 . . . 308(93)
COUP-TF
COUP/HNF-4 heterodimer


M00278
1933 . . . 1941(93)
Lmo2
complex of Lmo2 bound to Tal-1, E2A proteins, and





GATA-1, half-site 2


M00076
1932 . . . 1941(93)
GATA-2
GATA-binding factor 2



1303 . . . 1312(92)



743 . . . 734(92)



987 . . . 996(92)



925 . . . 916(90)


M00099
1813 . . . 1798(92)
S8
S8



1114 . . . 1129(90)


M00104
28 . . . 37(92)
CDP
cut-like homeodomain protein


M00223
547 . . . 539(92)
STATx
signal transducers and activators of transcription


M00271
1955 . . . 1960(92)
AML-1a
runt-factor AML-1


M00254
1831 . . . 1820(91)
CCAAT
cellular and viral CCAAT box


M00042
649 . . . 658(91)
Sox-5
Sox-5


M00289
384 . . . 396(91)
HFH-3
HNF-3/Fkh Homolog 3 (= Freac-6)


M00302
1384 . . . 1395(91)
NF-AT
Nuclear factor of activated T-cells



841 . . . 830(90)


M00155
367 . . . 382(91)
ARP-1
apolipoprotein AI regulatory protein 1


M00208
470 . . . 459(90)
NF-kappaB
NF-kappaB binding site


M00183
1030 . . . 1039(90)
c-Myb
c-Myb


M00240
243 . . . 237(90)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog



1454 . . . 1448(90)


M00188
1788 . . . 1798(90)
AP-1
activator protein 1


M00083
47 . . . 40(90)
MZF1
MZF1


M00184
273 . . . 282(90)
MyoD
myoblast determining factor


M00147
167 . . . 158(90)
HSF2
heat shock factor 2


M00087
984 . . . 995(90)
Ik-2
Ikaros 2


M00172
1788 . . . 1798(90)
AP-1
activator protein 1


M00221
1860 . . . 1850(90)
SREBP-1
sterol regulatory element-binding protein 1


M00194
471 . . . 458(90)
NF-kappaB
NF-kappaB
















TABLE 17







putative transcription factor binding motifs within the DUB regulatory or promoter,


region of hDUB 8.5. The position is indicated by nucleotides.










Transfac
Position(Score)
Name
Description





M00100
1105 . . . 1099(100)
CdxA
CdxA


M00241
1800 . . . 1807(100)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog


M00271
27 . . . 32(100)
AML-1a
runt-factor AML-1



1955 . . . 1960(92)


M00148
1020 . . . 1014(100)
SRY
sex-determining region Y gene product



970 . . . 976(100)



947 . . . 941(96)



1553 . . . 1559(92)



100 . . . 106(92)



141 . . . 135(90)



843 . . . 837(90)



1365 . . . 1359(90)



1719 . . . 1713(90)



1824 . . . 1818(90)


M00101
1105 . . . 1099(99)
CdxA
CdxA



833 . . . 827(98)



1234 . . . 1228(98)



1388 . . . 1382(98)



1300 . . . 1294(93)



1412 . . . 1418(92)



964 . . . 970(92)



1682 . . . 1688(91)



1688 . . . 1682(91)


M00278
618 . . . 610(98)
Lmo2
complex of Lmo2 bound to Tal-1, E2A proteins, and





GATA-1, half-site 2



1933 . . . 1941(93)


M00075
1838 . . . 1847(97)
GATA-1
GATA-binding factor 1



619 . . . 610(97)



1701 . . . 1692(95)



1889 . . . 1898(93)



903 . . . 894(91)



1736 . . . 1745(90)


M00054
442 . . . 451(96)
NF-
NF-kappaB



451 . . . 442(91)
kappaB


M00253
175 . . . 168(96)
cap
cap signal for transcription initiation



1794 . . . 1801(95)



1893 . . . 1886(95)



1455 . . . 1462(94)



798 . . . 805(94)



629 . . . 636(94)



1489 . . . 1482(92)



433 . . . 426(92)



1329 . . . 1322(91)



1877 . . . 1870(91)



921 . . . 928(91)



957 . . . 964(90)



1815 . . . 1808(90)



1302 . . . 1309(90)


M00272
1270 . . . 1279(96)
p53
tumor suppressor p53


M00096
1827 . . . 1819(96)
Pbx-1
Pbx-1


M00285
1734 . . . 1746(95)
TCF11
TCF11/KCR-F1/Nrf1 homodimers



1115 . . . 1127(91)



1490 . . . 1478(91)


M00076
619 . . . 610(95)
GATA-2
GATA-binding factor 2



1932 . . . 1941(93)



1701 . . . 1692(92)



1306 . . . 1315(92)



987 . . . 996(92)


M00077
1933 . . . 1941(95)
GATA-3
GATA-binding factor 3



618 . . . 610(92)


M00199
1797 . . . 1789(94)
AP-1
AP-1 binding site



1789 . . . 1797(91)


M00174
1788 . . . 1798(94)
AP-1
activator protein 1


M00083
566 . . . 559(93)
MZF1
MZF1


M00099
1813 . . . 1798(92)
S8
S8



1114 . . . 1129(90)


M00208
441 . . . 452(92)
NF-
NF-kappaB binding site




kappaB


M00033
808 . . . 795(92)
p300
p300


M00227
1677 . . . 1669(91)
v-Myb
v-Myb


M00254
1831 . . . 1820(91)
CCAAT
cellular and viral CCAAT box


M00183
166 . . . 157(91)
c-Myb
c-Myb



1030 . . . 1039(90)


M00267
102 . . . 89(91)
XFD-1
Xenopus fork head domain factor 1


M00240
1457 . . . 1451(90)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog



296 . . . 302(90)


M00188
1788 . . . 1798(90)
AP-1
activator protein 1


M00302
841 . . . 830(90)
NF-AT
Nuclear factor of activated T-cells


M00087
984 . . . 995(90)
Ik-2
Ikaros 2


M00172
1788 . . . 1798(90)
AP-1
activator protein 1


M00003
965 . . . 956(90)
v-Myb
v-Myb


M00221
1860 . . . 1850(90)
SREBP-1
sterol regulatory element-binding protein 1


M00053
441 . . . 450(90)
c-Rel
c-Rel
















TABLE 18







putative transcription factor binding motifs within the DUB regulatory or promoter,


region of hDUB 8.6. The position is indicated by nucleotides.










Transfac
Position(Score)
Name
Description





M00100
1105 . . . 1099(100)
CdxA
CdxA


M00241
1800 . . . 1807(100)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman





homolog


M00148
1020 . . . 1014(100)
SRY
sex-determining region Y gene product



970 . . . 976(100)



947 . . . 941(96)



1550 . . . 1556(92)



843 . . . 837(90)



707 . . . 713(90)



1362 . . . 1356(90)



1719 . . . 1713(90)



1824 . . . 1818(90)



395 . . . 389(90)



748 . . . 742(90)



300 . . . 306(90)


M00101
1105 . . . 1099(99)
CdxA
CdxA



833 . . . 827(98)



1385 . . . 1379(98)



1409 . . . 1415(92)



964 . . . 970(92)



726 . . . 720(92)



424 . . . 430(92)


M00075
1838 . . . 1847(97)
GATA-1
GATA-binding factor 1



1889 . . . 1898(93)



925 . . . 916(93)



1736 . . . 1745(90)


M00272
1267 . . . 1276(96)
p53
tumor suppressor p53


M00253
161 . . . 168(96)
cap
cap signal for transcription initiation



1794 . . . 1801(95)



484 . . . 491(95)



1893 . . . 1886(95)



1452 . . . 1459(94)



798 . . . 805(94)



748 . . . 755(94)



957 . . . 964(94)



1486 . . . 1479(92)



338 . . . 345(92)



1697 . . . 1704(92)



562 . . . 569(91)



1877 . . . 1870(91)



1815 . . . 1808(90)



321 . . . 328(90)



1326 . . . 1319(90)



1299 . . . 1306(90)


M00096
1827 . . . 1819(96)
Pbx-1
Pbx-1


M00285
1734 . . . 1746(95)
TCF11
TCF11/KCR-F1/Nrf1 homodimers



1115 . . . 1127(91)


M00077
1933 . . . 1941(95)
GATA-3
GATA-binding factor 3


M00054
469 . . . 460(95)
NF-kappaB
NF-kappaB


M00141
456 . . . 464(94)
Lyf-1
LyF-1


M00134
306 . . . 324(94)
HNF-4
hepatic nuclear factor 4


M00052
469 . . . 460(94)
NF-kappaB
NF-kappaB (p65)


M00199
1797 . . . 1789(94)
AP-1
AP-1 binding site



1789 . . . 1797(91)


M00174
1788 . . . 1798(94)
AP-1
activator protein 1


M00053
469 . . . 460(94)
c-Rel
c-Rel


M00033
758 . . . 745(94)
p300
p300



808 . . . 795(92)


M00158
321 . . . 308(93)
COUP-TF
COUP/HNF-4 heterodimer


M00278
1933 . . . 1941(93)
Lmo2
complex of Lmo2 bound to Tal-1, E2A proteins,





and GATA-1, half-site 2


M00076
1932 . . . 1941(93)
GATA-2
GATA-binding factor 2



1303 . . . 1312(92)



743 . . . 734(92)



987 . . . 996(92)



925 . . . 916(90)


M00099
1813 . . . 1798(92)
S8
S8



1114 . . . 1129(90)


M00104
28 . . . 37(92)
CDP
cut-like homeodomain protein


M00223
547 . . . 539(92)
STATx
signal transducers and activators of transcription


M00271
1955 . . . 1960(92)
AML-1a
runt-factor AML-1


M00254
1831 . . . 1820(91)
CCAAT
cellular and viral CCAAT box


M00042
649 . . . 658(91)
Sox-5
Sox-5


M00289
384 . . . 396(91)
HFH-3
HNF-3/Fkh Homolog 3 (= Freac-6)


M00302
1384 . . . 1395(91)
NF-AT
Nuclear factor of activated T-cells



841 . . . 830(90)


M00155
367 . . . 382(91)
ARP-1
apolipoprotein AI regulatory protein 1


M00208
470 . . . 459(90)
NF-kappaB
NF-kappaB binding site


M00183
1030 . . . 1039(90)
c-Myb
c-Myb


M00240
243 . . . 237(90)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman





homolog



1454 . . . 1448(90)


M00188
1788 . . . 1798(90)
AP-1
activator protein 1


M00083
47 . . . 40(90)
MZF1
MZF1


M00184
273 . . . 282(90)
MyoD
myoblast determining factor


M00147
167 . . . 158(90)
HSF2
heat shock factor 2


M00087
984 . . . 995(90)
Ik-2
Ikaros 2


M00172
1788 . . . 1798(90)
AP-1
activator protein 1


M00221
1860 . . . 1850(90)
SREBP-1
sterol regulatory element-binding protein 1


M00194
471 . . . 458(90)
NF-kappaB
NF-kappaB
















TABLE 19







putative transcription factor binding motifs within the DUB regulatory or promoter,


region of hDUB 8.7. The position is indicated by nucleotides.










Transfac
Position(Score)
Name
Description





M00349
94 . . . 103(100)
GATA-2
GATA-binding factor 2


M00348
94 . . . 103(100)
GATA-2
GATA-binding factor 2


M00241
1800 . . . 1807(100)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog


M00100
1102 . . . 1096(100)
CdxA
CdxA


M00148
1017 . . . 1011(100)
SRY
sex-determining region Y gene product



967 . . . 973(100)



704 . . . 710(100)



944 . . . 938(96)



1550 . . . 1556(92)



840 . . . 834(90)



1362 . . . 1356(90)



1719 . . . 1713(90)



1824 . . . 1818(90)



392 . . . 386(90)



745 . . . 739(90)



298 . . . 304(90)


M00350
94 . . . 103(100)
GATA-3
GATA-binding factor 3


M00101
1102 . . . 1096(99)
CdxA
CdxA



830 . . . 824(98)



1231 . . . 1225(98)



1385 . . . 1379(98)



1297 . . . 1291(93)



1409 . . . 1415(92)



723 . . . 717(92)



961 . . . 967(92)



66 . . . 60(92)



421 . . . 427(92)



1682 . . . 1688(91)



1688 . . . 1682(91)


M00203
96 . . . 106(98)
GATA-X
GATA binding site


M00347
94 . . . 103(97)
GATA-1
GATA-binding factor 1


M00075
1838 . . . 1847(97)
GATA-1
GATA-binding factor 1



1701 . . . 1692(95)



1889 . . . 1898(93)



900 . . . 891(91)



138 . . . 129(90)



1736 . . . 1745(90)


M00158
319 . . . 306(96)
COUP-TF
COUP/HNF-4 heterodimer


M00272
1267 . . . 1276(96)
p53
tumor suppressor p53


M00134
304 . . . 322(96)
HNF-4
hepatic nuclear factor 4


M00096
1827 . . . 1819(96)
Pbx-1
Pbx-1


M00285
1734 . . . 1746(95)
TCF11
TCF11/KCR-F1/Nrf1 homodimers



1112 . . . 1124(91)



1487 . . . 1475(91)



13 . . . 1(90)


M00077
1933 . . . 1941(95)
GATA-3
GATA-binding factor 3


M00253
1794 . . . 1801(95)
cap
cap signal for transcription initiation



481 . . . 488(95)



1893 . . . 1886(95)



1452 . . . 1459(94)



795 . . . 802(94)



656 . . . 649(93)



1486 . . . 1479(92)



1326 . . . 1319(91)



559 . . . 566(91)



1877 . . . 1870(91)



745 . . . 752(91)



918 . . . 925(91)



954 . . . 961(90)



1815 . . . 1808(90)



1299 . . . 1306(90)


M00054
466 . . . 457(95)
NF-kappaB
NF-kappaB


M00146
165 . . . 156(94)
HSF1
heat shock factor 1


M00147
165 . . . 156(94)
HSF2
heat shock factor 2



156 . . . 165(94)


M00141
453 . . . 461(94)
Lyf-1
LyF-1


M00052
466 . . . 457(94)
NF-kappaB
NF-kappaB (p65)


M00199
1797 . . . 1789(94)
AP-1
AP-1 binding site



1789 . . . 1797(91)


M00174
1788 . . . 1798(94)
AP-1
activator protein 1


M00053
466 . . . 457(94)
c-Rel
c-Rel


M00278
1933 . . . 1941(93)
Lmo2
complex of Lmo2 bound to Tal-1, E2A proteins, and





GATA-1, half-site 2


M00076
1932 . . . 1941(93)
GATA-2
GATA-binding factor 2



1701 . . . 1692(92)



1303 . . . 1312(92)



984 . . . 993(92)


M00099
1813 . . . 1798(92)
S8
S8



1111 . . . 1126(90)


M00184
271 . . . 280(92)
MyoD
myoblast determining factor


M00223
544 . . . 536(92)
STATx
signal transducers and activators of transcription


M00073
36 . . . 46(92)
deltaEF1
deltaEF1


M00033
805 . . . 792(92)
p300
p300


M00271
1955 . . . 1960(92)
AML-1a
runt-factor AML-1


M00254
1831 . . . 1820(91)
CCAAT
cellular and viral CCAAT box


M00277
281 . . . 270(91)
Lmo2
complex of Lmo2 bound to Tal-1, E2A proteins, and





GATA-1, half-site 1


M00289
381 . . . 393(91)
HFH-3
HNF-3/Fkh Homolog 3 (= Freac-6)


M00208
467 . . . 456(90)
NF-kappaB
NF-kappaB binding site


M00183
1027 . . . 1036(90)
c-Myb
c-Myb


M00240
241 . . . 235(90)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog



1454 . . . 1448(90)


M00188
1788 . . . 1798(90)
AP-1
activator protein 1


M00302
838 . . . 827(90)
NF-AT
Nuclear factor of activated T-cells


M00128
93 . . . 105(90)
GATA-1
GATA-binding factor 1


M00087
981 . . . 992(90)
Ik-2
Ikaros 2


M00172
1788 . . . 1798(90)
AP-1
activator protein 1


M00042
69 . . . 78(90)
Sox-5
Sox-5


M00003
962 . . . 953(90)
v-Myb
v-Myb


M00221
1860 . . . 1850(90)
SREBP-1
sterol regulatory element-binding protein 1


M00194
468 . . . 455(90)
NF-kappaB
NF-kappaB
















TABLE 20







putative transcription factor binding motifs within the DUB regulatory or promoter,


region of hDUB 8.8. The position is indicated by nucleotides.










Transfac
Position(Score)
Name
Description





M00148
1020 . . . 1014(100)
SRY
sex-determining region Y gene product



970 . . . 976(100)



947 . . . 941(96)



1550 . . . 1556(92)



843 . . . 837(90)



707 . . . 713(90)



1362 . . . 1356(90)



1719 . . . 1713(90)



1824 . . . 1818(90)



395 . . . 389(90)



748 . . . 742(90)



300 . . . 306(90)


M00241
1800 . . . 1807(100)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog


M00100
1105 . . . 1099(100)
CdxA
CdxA


M00101
1105 . . . 1099(99)
CdxA
CdxA



833 . . . 827(98)



1385 . . . 1379(98)



1409 . . . 1415(92)



964 . . . 970(92)



726 . . . 720(92)



424 . . . 430(92)


M00075
1838 . . . 1847(97)
GATA-1
GATA-binding factor 1



1889 . . . 1898(93)



925 . . . 916(93)



1736 . . . 1745(90)


M00272
1267 . . . 1276(96)
p53
tumor suppressor p53


M00253
161 . . . 168(96)
cap
cap signal for transcription initiation



1794 . . . 1801(95)



484 . . . 491(95)



1893 . . . 1886(95)



1452 . . . 1459(94)



798 . . . 805(94)



748 . . . 755(94)



957 . . . 964(94)



1486 . . . 1479(92)



338 . . . 345(92)



1697 . . . 1704(92)



562 . . . 569(91)



1877 . . . 1870(91)



1815 . . . 1808(90)



321 . . . 328(90)



1326 . . . 1319(90)



1299 . . . 1306(90)


M00096
1827 . . . 1819(96)
Pbx-1
Pbx-1


M00285
1734 . . . 1746(95)
TCF11
TCF11/KCR-F1/Nrf1 homodimers



1115 . . . 1127(91)


M00077
1933 . . . 1941(95)
GATA-3
GATA-binding factor 3


M00054
469 . . . 460(95)
NF-kappaB
NF-kappaB


M00141
456 . . . 464(94)
Lyf-1
LyF-1


M00134
306 . . . 324(94)
HNF-4
hepatic nuclear factor 4


M00052
469 . . . 460(94)
NF-kappaB
NF-kappaB (p65)


M00199
1797 . . . 1789(94)
AP-1
AP-1 binding site



1789 . . . 1797(91)


M00174
1788 . . . 1798(94)
AP-1
activator protein 1


M00053
469 . . . 460(94)
c-Rel
c-Rel


M00033
758 . . . 745(94)
p300
p300



808 . . . 795(92)


M00158
321 . . . 308(93)
COUP-TF
COUP/HNF-4 heterodimer


M00278
1933 . . . 1941(93)
Lmo2
complex of Lmo2 bound to Tal-1, E2A proteins, and





GATA-1, half-site 2


M00076
1932 . . . 1941(93)
GATA-2
GATA-binding factor 2



1303 . . . 1312(92)



743 . . . 734(92)



925 . . . 916(90)


M00099
1813 . . . 1798(92)
S8
S8



1114 . . . 1129(90)


M00104
28 . . . 37(92)
CDP
cut-like homeodomain protein


M00223
547 . . . 539(92)
STATx
signal transducers and activators of transcription


M00271
1955 . . . 1960(92)
AML-1a
runt-factor AML-1


M00254
1831 . . . 1820(91)
CCAAT
cellular and viral CCAAT box


M00042
649 . . . 658(91)
Sox-5
Sox-5


M00289
384 . . . 396(91)
HFH-3
HNF-3/Fkh Homolog 3 (= Freac-6)


M00302
1384 . . . 1395(91)
NF-AT
Nuclear factor of activated T-cells



841 . . . 830(90)


M00155
367 . . . 382(91)
ARP-1
apolipoprotein AI regulatory protein 1


M00208
470 . . . 459(90)
NF-kappaB
NF-kappaB binding site


M00183
1030 . . . 1039(90)
c-Myb
c-Myb


M00240
243 . . . 237(90)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog



1454 . . . 1448(90)


M00188
1788 . . . 1798(90)
AP-1
activator protein 1


M00083
47 . . . 40(90)
MZF1
MZF1


M00184
273 . . . 282(90)
MyoD
myoblast determining factor


M00147
167 . . . 158(90)
HSF2
heat shock factor 2


M00172
1788 . . . 1798(90)
AP-1
activator protein 1


M00221
1860 . . . 1850(90)
SREBP-1
sterol regulatory element-binding protein 1


M00194
471 . . . 458(90)
NF-kappaB
NF-kappaB
















TABLE 21







putative transcription factor binding motifs within the DUB regulatory or promoter,


region of hDUB 8.9. The position is indicated by nucleotides.










Transfac
Position(Score)
Name
Description





M00148
991 . . . 997(100)
SRY
sex-determining region Y gene product



1040 . . . 1034(100)



967 . . . 961(96)



1576 . . . 1582(92)



1550 . . . 1556(92)



1385 . . . 1379(90)



1824 . . . 1818(90)



13 . . . 19(90)



415 . . . 409(90)



727 . . . 733(90)


M00101
1125 . . . 1119(100)
CdxA
CdxA



1254 . . . 1248(98)



1167 . . . 1161(97)



542 . . . 548(97)



884 . . . 878(94)



1432 . . . 1438(93)



743 . . . 737(92)



89 . . . 83(92)



592 . . . 586(92)



1280 . . . 1286(92)



444 . . . 450(92)



1682 . . . 1688(91)



1688 . . . 1682(91)


M00083
779 . . . 772(100)
MZF1
MZF1



68 . . . 61(90)


M00241
1800 . . . 1807(100)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog


M00272
1290 . . . 1299(96)
p53
tumor suppressor p53


M00253
182 . . . 189(96)
cap
cap signal for transcription initiation



1794 . . . 1801(95)



1893 . . . 1886(95)



1475 . . . 1482(94)



768 . . . 775(94)



1506 . . . 1499(93)



1349 . . . 1342(91)



582 . . . 589(91)



351 . . . 358(90)



1815 . . . 1808(90)



342 . . . 349(90)



1877 . . . 1870(90)



504 . . . 511(90)



1322 . . . 1329(90)


M00100
1125 . . . 1119(96)
CdxA
CdxA


M00042
742 . . . 751(96)
Sox-5
Sox-5



669 . . . 678(92)



726 . . . 735(92)


M00096
1827 . . . 1819(96)
Pbx-1
Pbx-1


M00077
1933 . . . 1941(95)
GATA-3
GATA-binding factor 3


M00045
1877 . . . 1888(95)
E4BP4
E4BP4


M00054
489 . . . 480(95)
NF-kappaB
NF-kappaB


M00141
476 . . . 484(94)
Lyf-1
LyF-1


M00052
489 . . . 480(94)
NF-kappaB
NF-kappaB (p65)


M00199
1797 . . . 1789(94)
AP-1
AP-1 binding site



1789 . . . 1797(91)


M00174
1788 . . . 1798(94)
AP-1
activator protein 1


M00053
489 . . . 480(94)
c-Rel
c-Rel


M00278
1933 . . . 1941(93)
Lmo2
complex of Lmo2 bound to Tal-1, E2A proteins, and





GATA-1, half-site 2


M00076
1932 . . . 1941(93)
GATA-2
GATA-binding factor 2



1007 . . . 1016(92)



1701 . . . 1692(91)


M00285
1734 . . . 1746(92)
TCF11
TCF11/KCR-F1/Nrf1 homodimers



1135 . . . 1147(91)


M00099
1813 . . . 1798(92)
S8
S8



1134 . . . 1149(90)


M00104
49 . . . 58(92)
CDP
cut-like homeodomain protein


M00223
567 . . . 559(92)
STATx
signal transducers and activators of transcription


M00075
1701 . . . 1692(92)
GATA-1
GATA-binding factor 1



161 . . . 152(90)



1736 . . . 1745(90)


M00348
316 . . . 325(92)
GATA-2
GATA-binding factor 2


M00109
873 . . . 886(91)
C/EBPbeta
CCAAT/enhancer binding protein beta


M00254
1831 . . . 1820(91)
CCAAT
cellular and viral CCAAT box


M00203
318 . . . 328(91)
GATA-X
GATA binding site


M00350
316 . . . 325(91)
GATA-3
GATA-binding factor 3


M00289
404 . . . 416(91)
HFH-3
HNF-3/Fkh Homolog 3 (= Freac-6)


M00113
833 . . . 822(90)
CREB
cAMP-responsive element binding protein


M00249
1165 . . . 1153(90)
CHOP-
heterodimers of CHOP and C/EBPalpha




C/EBPalpha


M00208
490 . . . 479(90)
NF-kappaB
NF-kappaB binding site


M00190
1263 . . . 1250(90)
C/EBP
CCAAT/enhancer binding factor


M00349
316 . . . 325(90)
GATA-2
GATA-binding factor 2


M00116
1263 . . . 1250(90)
C/EBPalpha
CCAAT/enhancer binding protein alpha


M00183
1050 . . . 1059(90)
c-Myb
c-Myb


M00240
263 . . . 257(90)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog



1477 . . . 1471(90)


M00188
1788 . . . 1798(90)
AP-1
activator protein 1


M00302
1407 . . . 1418(90)
NF-AT
Nuclear factor of activated T-cells


M00184
293 . . . 302(90)
MyoD
myoblast determining factor


M00147
188 . . . 179(90)
HSF2
heat shock factor 2


M00087
1004 . . . 1015(90)
Ik-2
Ikaros 2


M00172
1788 . . . 1798(90)
AP-1
activator protein 1


M00221
1860 . . . 1850(90)
SREBP-1
sterol regulatory element-binding protein 1


M00033
778 . . . 765(90)
p300
p300


M00194
491 . . . 478(90)
NF-kappaB
NF-kappaB
















TABLE 22







putative transcription factor binding motifs within the DUB regulatory or promoter,


region of hDUB 8.10. The position is indicated by nucleotides.










Transfac
Position(Score)
Name
Description





M00148
1038 . . . 1032(100)
SRY
sex-determining region Y gene product



965 . . . 959(96)



1550 . . . 1556(92)



725 . . . 731(90)



1382 . . . 1376(90)



310 . . . 316(90)



1715 . . . 1709(90)



1824 . . . 1818(90)



12 . . . 18(90)



413 . . . 407(90)



1630 . . . 1624(90)



319 . . . 325(90)


M00241
1800 . . . 1807(100)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog


M00100
1123 . . . 1117(100)
CdxA
CdxA


M00240
1240 . . . 1234(100)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog



262 . . . 256(90)


M00141
474 . . . 482(100)
Lyf-1
LyF-1


M00101
1123 . . . 1117(99)
CdxA
CdxA



540 . . . 546(97)



1429 . . . 1435(94)



982 . . . 988(92)



88 . . . 82(92)



741 . . . 735(92)



442 . . . 448(92)


M00075
1838 . . . 1847(97)
GATA-1
GATA-binding factor 1



1889 . . . 1898(93)



1736 . . . 1745(90)


M00253
766 . . . 773(96)
cap
cap signal for transcription initiation



181 . . . 188(96)



1794 . . . 1801(95)



1893 . . . 1886(95)



1210 . . . 1217(94)



816 . . . 823(94)



1506 . . . 1499(92)



357 . . . 364(92)



1697 . . . 1704(92)



1090 . . . 1097(91)



1346 . . . 1339(91)



1877 . . . 1870(91)



71 . . . 78(90)



580 . . . 587(90)



1815 . . . 1808(90)



340 . . . 347(90)



502 . . . 509(90)



1319 . . . 1326(90)


M00096
1827 . . . 1819(96)
Pbx-1
Pbx-1


M00285
1734 . . . 1746(95)
TCF11
TCF11/KCR-F1/Nrf1 homodimers



1133 . . . 1145(91)



35 . . . 23(91)



1089 . . . 1101(90)


M00134
325 . . . 343(94)
HNF-4
hepatic nuclear factor 4


M00199
1797 . . . 1789(94)
AP-1
AP-1 binding site



1789 . . . 1797(91)


M00174
1788 . . . 1798(94)
AP-1
activator protein 1


M00042
740 . . . 749(94)
Sox-5
Sox-5



1631 . . . 1622(92)



667 . . . 676(91)


M00106
672 . . . 681(94)
CDP
cut-like homeodomain protein


M00158
340 . . . 327(93)
COUP-TF
COUP/HNF-4 heterodimer


M00076
761 . . . 752(93)
GATA-2
GATA-binding factor 2



1323 . . . 1332(92)



1005 . . . 1014(92)


M00099
1813 . . . 1798(92)
S8
S8



1132 . . . 1147(90)


M00104
48 . . . 57(92)
CDP
cut-like homeodomain protein


M00223
565 . . . 557(92)
STATx
signal transducers and activators of transcription


M00033
826 . . . 813(92)
p300
p300


M00271
1955 . . . 1960(92)
AML-1a
runt-factor AML-1


M00254
1831 . . . 1820(91)
CCAAT
cellular and viral CCAAT box


M00289
402 . . . 414(91)
HFH-3
HNF-3/Fkh Homolog 3 (= Freac-6)


M00217
160 . . . 153(90)
USF
USF binding site


M00183
1048 . . . 1057(90)
c-Myb
c-Myb


M00188
1788 . . . 1798(90)
AP-1
activator protein 1


M00083
67 . . . 60(90)
MZF1
MZF1


M00184
292 . . . 301(90)
MyoD
myoblast determining factor


M00147
187 . . . 178(90)
HSF2
heat shock factor 2


M00087
1002 . . . 1013(90)
Ik-2
Ikaros 2


M00172
1788 . . . 1798(90)
AP-1
activator protein 1


M00221
1860 . . . 1850(90)
SREBP-1
sterol regulatory element-binding protein 1
















TABLE 23







putative transcription factor binding motifs within the DUB regulatory or promoter,


region of hDUB 8.11. The position is indicated by nucleotides.










Transfac
Position(Score)
Name
Description





M00348
71 . . . 80(100)
GATA-2
GATA-binding factor 2


M00350
71 . . . 80(100)
GATA-3
GATA-binding factor 3


M00349
71 . . . 80(100)
GATA-2
GATA-binding factor 2


M00148
990 . . . 984(100)
SRY
sex-determining region Y gene product



1664 . . . 1658(100)



813 . . . 807(96)



917 . . . 911(96)



1858 . . . 1864(92)



1850 . . . 1856(92)



1836 . . . 1842(92)



1399 . . . 1405(90)



1514 . . . 1508(90)



680 . . . 686(90)



2104 . . . 2098(90)



368 . . . 362(90)



721 . . . 715(90)



1002 . . . 996(90)



1910 . . . 1904(90)



274 . . . 280(90)


M00100
595 . . . 589(100)
CdxA
CdxA



1408 . . . 1402(100)



1474 . . . 1480(96)


M00101
595 . . . 589(99)
CdxA
CdxA



1408 . . . 1402(99)



803 . . . 797(98)



1537 . . . 1531(98)



1715 . . . 1721(92)



699 . . . 693(92)



934 . . . 940(92)



43 . . . 37(92)



495 . . . 501(92)


M00141
1282 . . . 1274(98)
Lyf-1
LyF-1


M00347
71 . . . 80(97)
GATA-1
GATA-binding factor 1


M00272
1573 . . . 1582(96)
p53
tumor suppressor p53


M00253
1137 . . . 1144(96)
cap
cap signal for transcription initiation



136 . . . 143(96)



2074 . . . 2081(95)



457 . . . 464(95)



2173 . . . 2166(95)



721 . . . 728(94)



1444 . . . 1437(94)



660 . . . 653(94)



1792 . . . 1785(92)



312 . . . 319(92)



1632 . . . 1625(91)



535 . . . 542(91)



2095 . . . 2088(91)



1358 . . . 1365(91)



768 . . . 775(90)



295 . . . 302(90)



2157 . . . 2150(90)


M00096
2107 . . . 2099(96)
Pbx-1
Pbx-1


M00285
2014 . . . 2026(95)
TCF11
TCF11/KCR-F1/Nrf1 homodimers



1418 . . . 1430(91)


M00130
1657 . . . 1668(95)
HFH-2
HNF-3/Fkh Homolog 2


M00077
2213 . . . 2221(95)
GATA-3
GATA-binding factor 3


M00054
442 . . . 433(95)
NF-kappaB
NF-kappaB


M00052
442 . . . 433(94)
NF-kappaB
NF-kappaB (p65)


M00203
73 . . . 83(94)
GATA-X
GATA binding site


M00199
2077 . . . 2069(94)
AP-1
AP-1 binding site



2069 . . . 2077(91)



1994 . . . 2002(90)


M00174
2068 . . . 2078(94)
AP-1
activator protein 1



1436 . . . 1446(90)


M00075
895 . . . 886(94)
GATA-1
GATA-binding factor 1



2169 . . . 2178(93)



1091 . . . 1082(93)



1981 . . . 1972(92)



2016 . . . 2025(90)


M00053
442 . . . 433(94)
c-Rel
c-Rel


M00241
2080 . . . 2087(94)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog


M00076
716 . . . 707(94)
GATA-2
GATA-binding factor 2



2212 . . . 2221(93)



1609 . . . 1618(92)



957 . . . 966(92)



895 . . . 886(91)



1981 . . . 1972(91)


M00106
627 . . . 636(94)
CDP
cut-like homeodomain protein


M00033
731 . . . 718(94)
p300
p300


M00227
2149 . . . 2141(94)
v-Myb
v-Myb


M00158
295 . . . 282(93)
COUP-TF
COUP/HNF-4 heterodimer


M00162
2080 . . . 2093(93)
Oct-1
octamer-binding factor 1


M00278
2213 . . . 2221(93)
Lmo2
complex of Lmo2 bound to Tal-1, E2A proteins, and





GATA- 1, half-site 2


M00134
280 . . . 298(93)
HNF-4
hepatic nuclear factor 4


M00032
226 . . . 235(93)
c-Ets-1(p54)
c-Ets-1(p54)


M00172
1436 . . . 1446(92)
AP-1
activator protein 1



2068 . . . 2078(90)


M00117
1089 . . . 1076(92)
C/EBPbeta
CCAAT/enhancer binding protein beta


M00223
520 . . . 512(92)
STATx
signal transducers and activators of transcription


M00042
1911 . . . 1902(92)
Sox-5
Sox-5



622 . . . 631(91)


M00073
13 . . . 23(92)
deltaEF1
deltaEF1


M00188
1436 . . . 1446(91)
AP-1
activator protein 1



2068 . . . 2078(90)


M00254
2111 . . . 2100(91)
CCAAT
cellular and viral CCAAT box


M00099
2093 . . . 2078(91)
S8
S8



2076 . . . 2091(90)



1417 . . . 1432(90)


M00289
1657 . . . 1669(91)
HFH-3
HNF-3/Fkh Homolog 3 (=Freac-6)



357 . . . 369(91)


M00147
752 . . . 743(91)
HSF2
heat shock factor 2



142 . . . 133(90)


M00208
443 . . . 432(90)
NF-kappaB
NF-kappaB binding site


M00217
115 . . . 108(90)
USF
USF binding site


M00183
1333 . . . 1342(90)
c-Myb
c-Myb


M00173
1436 . . . 1446(90)
AP-1
activator protein 1


M00240
217 . . . 211(90)
Nkx-2.5
homeo domain factor Nkx-2.5/Csx, tinman homolog


M00184
1965 . . . 1974(90)
MyoD
myoblast determining factor



247 . . . 256(90)


M00087
954 . . . 965(90)
Ik-2
Ikaros 2


M00128
70 . . . 82(90)
GATA-1
GATA-binding factor 1


M00145
1347 . . . 1362(90)
Brn-2
POU factor Brn-2


M00194
444 . . . 431(90)
NF-kappaB
NF-kappaB









REFERENCES 


    1. Baek, K. H., Mondoux, M. A., Jaster, R., Fire-Levin, E., and D'Andrea, A. D. (2001). DUB-2A, a new member of the DUB subfamily of hematopoietic deubiquitinating enzymes, Blood 98, 636–42.
    2. Jaster, R., Baek, K. H., and D'Andrea, A. D. (1999). Analysis of cis-acting sequences and trans-acting factors regulating the interleukin-3 response element of the DUB-1 gene, Biochim Biophys Acta 1446, 308–16.
    3. Jaster, R., Zhu, Y., Pless, M., Bhattacharya, S., Mathey-Prevot, B., and D'Andrea, A. D. (1997). JAK2 is required for induction of the murine DUB-1 gene, Mol Cell Biol 17, 3364–72.
    4. Migone, T. S., Humbert, M., Rascle, A., Sanden, D., D'Andrea, A., Johnston, J. A., Baek, K. H., Mondoux, M. A., Jaster, R., Fire-Levin, E., et al. (2001). The deubiquitinating enzyme DUB-2 prolongs cytokine-induced signal transducers and activators of transcription activation and suppresses apoptosis following cytokine withdrawal, Blood 98, 1935–41.
    5. Zhu, Y., Carroll, M., Papa, F. R., Hochstrasser, M., and D'Andrea, A. D. (1996a). DUB-1, a deubiquitinating enzyme with growth-suppressing activity, Proc Natl Acad Sci USA 93, 3275–9.
    6. Zhu, Y., Lambert, K., Corless, C., Copeland, N. G., Gilbert, D. J., Jenkins, N. A., and D'Andrea, A. D. (1997). DUB-2 is a member of a novel family of cytokine-inducible deubiquitinating enzymes, J Biol Chem 272, 51–7.
    7. Zhu, Y., Pless, M., Inhorn, R., Mathey-Prevot, B., and D'Andrea, A. D. (1996b). The murine DUB-1 gene is specifically induced by the betac subunit of interleukin-3 receptor, Mol Cell Biol 16, 4808–17.









TABLE 24





Deduced Amino acid alignment of hDUB4.10 (Seq ID NO. 22)


and hDUB4.11 (Seq ID NO. 24).


















hDUB4.10
MCIRTGSPCDVCENYSVMSMTGRQLIDWAPLKIGYEHSSTPMPREHVHFRQHYNFGTKCA
60



hDUB4.11
MCIRTGSPCDVCENYSVMSMTGRQLIDWAPLKIGYEHSSTPMPRT-LYIRHRK-------
52



********************************************  :::*::


 


hDUB4.10
NCNSTIQCVTGNGGNIADPERSMRESRICTAYFGLFPLKQGPVLKMVISLGQRINRLNVE
120


hDUB4.11
---------PSDGAHLAHEK-------------------------------------TRE
66



         ..:*.::*. :                                     . *


 


hDUB4.10
RLSLEGKKIRCAKYYTSLTILRSESALSTSCPSVAERMMAAAKRIASFCNLRSQQKNLVI
180


hDUB4.11
RNGAKGKKIRCAKYYTSLTILRSESALSSSCPSVAERMMAAAK-----------------
109



* . :***********************:**************


 


hDUB4.10
LVPVDMEDDSLYLGGEWQFNHFSKLTSSRPDAAFAEIQRTSLPEKSPLSCETRVDLCDDL
240


hDUB4.11
---IDMEDDSLYLGGEWQFNHFSKLTSSRPDAAFAEIQRTSLPEKSPLS--------YDL
158



:********************************************* **         **


 


hDUB4.10
APVARQLAPREKLPLSSRRPAAVGAGLQNMGNTCYVNASLQCLTYTTPLANYMLSREHSQ
300


hDUB4.11
APVARQLAPREKLPLSSRRPAAVGAGLQNMGNTCYVNASLQCLTYTPPLANYMLSREHSQ
218



**********************************************.*************


 


hDUB4.10
TCHRHKGCMLCTMQAHITRALHNPGHVIQPSQALAAGFHRGKQEDAHEFLMFTVDAMKKA
360


hDUB4.11
TCHRHKGCMLCTMQAHITRALHNPGHVIQPSQALAAGFHRGKQEDAHEFLMFTVDAMKKA
278



************************************************************


 


hDUB4.10
CLPGHKQVDHHSKDTTLIHQIFGGYWRSQIKCLHCHGISDTFDPYLDIALDIQAAQSVQQ
420


hDUB4.11
CLPRHKQVDHHSKDTTLIHQIFGGYWRSQIKCLHCHGISDTFDPYLDIALDIQAAQSVQQ
338



*** ********************************************************


 


hDUB4.10
ALEQLVKPEELNGENAYHSGVCLQRAPASKTLTLHTSAKVLILVLKRFSDVTGNKIAKNV
480


hDUB4.11
ALEQLVKPEELNGENAYHCGVCLQRAPASKTLTLHTSAKVLILVLKRFSDVTGNKIAKNV
398



******************.*****************************************


 


hDUB4.10
QYPECLDMQPYMSQQNTGPLVYVLYAVLVHAGWSCHNGHYFSYVKAQEGQWYKMDDAEVT
540


hDUB4.11
QYPECLDMQPYMSQQNTGPLVYVLYAVLVHAEWSCHNGHYFSYVKAQEGQWYKMDDAEVT
458



******************************* ****************************


 


hDUB4.10
AASITSALSQQAYVLFYIQKSEWERHSESVSRGREPRALGTEDTDRRATQGELKRDHPCL
600


hDUB4.11
AASITSVLSQQAYVLFYIQKSEWERHSESVSRGREPRALGAEDTDRRATQGELKRDHPCL
518



******.*********************************:*******************


 


hDUB4.10
QAPELDEHLVERATQESTLDHWKFLQEQNKTKPEFNVRKVEGTLPPDVLVIHQSKYKCGM
660


hDUB4.11
QAPELDEHLVERATQESTLDHWKFLQEQNKTKPEFNVRKVKGTLPPDVLVIHQSKYKCGM
578



****************************************:*******************


 


hDUB4.10
KNHHPEQQSSLLNLSSSTPTHQESMNTGTLASLRGRARRSKGKNKHSKRALLVCQ 715


hDUB4.11
KNHHPEQQSSLLNLSSSTPTHQESMNTGTLASLRGRARRSKGKNKHSKRALLVC- 632



******************************************************

















TABLE 25





Nucleotide sequence alignment of hDUB4.5 (Seq ID NO. 13),



hDUB4.8 (Seq ID NO. 19) and hDUB8.2 (Seq ID NO. 43).


In frame termination codons in hDUB8.2 are underlined


















hDUB4.5
ATGCG-CCAGAGAGCTCGTCATTTGAAGACTCTCTCGGAAGGGATAGCGTCTTTCTGCAA
59



hDUB4.8
ATGCG-CCAGAGAGCTCGTCATTTGAAGACTCTCTCGGAACGGATAGCGTCTTGCTGCAA
59


hDUB8.2
ATGCGGCCAGAGAGCCCGTCATTTGAAGA----CTCGGAAGAGATAGCGTCTTTCTGCAA
56



***** ********* *************    ******** *********** ******


 


hDUB4.5
CCTGCGGTCCCAGCAGAAAAACCTTGTGATCCTTGTTCCAGTCGACATGGAGGAAGACTC
119


hDUB4.8
ACTGCGGTCCCAGCAGAAAAACCTTGTGATCCTTGTTCCAGTCGACATGGAGGACGACTC
119


hDUB8.2
CCTGCGGTCCCAGCCGAAAAACCTTGTGATCCTTGTTCCGGGCGACATGGAGGACGACTC
116



 ************* ************************ * ************ *****


 


hDUB4.5
ACTCTACTTGGGAGGTGAGTGGCAGTTCAACCACTTTTCAAAACTCACATCTTCTCGGCC
179


hDUB4.8
ACTCTACTTGGGAGGTGAGTGGCAGTTCAACCACTTTTCAAAACTCACATCTTCTCGGCC
179


hDUB8.2
ACTCTACTTGGGAGGTGAGTGGCAGTTCAACCACTTTTCAAAACTCACATCTTCTCGGCC
176



************************************************************


 


hDUB4.5
CGATGCAGCTTTTGCTGAAATCCAGCGGACTTCTCTCCCTGAGAAGTCACCACTCTCATG
239


hDUB4.8
CGATGCAGCTTTTGCTGAAATCCAGCGGACTTCTCTCCCTGAGAAGTCACCACTCTCATG
239


hDUB8.2
AGATGCAGCTTTTGCTGAAATCCAGCGGACTTCTCTCTCTGAGAAGTCATCACTCTCATC
236



 ************************************ *********** *********


 


hDUB4.5
TGAGACCCGTGTCGACCTCTGTGATGATTTGGCTCCTGTGGCAAGACAGCTTGCTCCCAG
299


hDUB4.8
TGAGACCCGTGTCGACCTCTGTGATGATTTGGCTCCTGTGGCAAGACAGCTTGCTCCCAG
299


hDUB8.2
TGAGACCCGCGTCGACCTCTGTGATGATTTGGCTCCTGTGGCAAGACAGCTCGCTCCCAG
296



********* ***************************************** ********


 


hDUB4.5
GGAGAAGCTTCCTCTGAGTAACAGGAGACCTGCTGCGGTGGGGGCTGGGCTCCAGAATAT
359


hDUB4.8
GGAGAAGCTTCCTCTGAGTAGCAGGAGACCTGCTGCGGTGGGGGCTGGGCTCCAGAATAT
359


hDUB8.2
GGAGAAGCTTCCTCTGAGTAGCAGGAGACCTGCTGCGGTGGGGGCTGGGCTCCAGAATAT
356



******************** ***************************************


 


hDUB4.5
GGGAAATACCTGCTACGTGAACGCTTCCTTGCAGTGCCTGACATACACACCGCCCCTTGC
419


hDUB4.8
GGGAAATACCTGCTACGTGAACGCTTCCTTGCAGTGCCTGACATACACACCGCCCCTTGC
419


hDUB8.2
GGGAAATACCTGCTACGTGAACGCTTCCCTGCAGTGCCTGACATACACACCGCCCCTTGC
416



**************************** *******************************


 


hDUB4.5
CAACTACATGCTGTCCCGGGAGCACTCTCAAACGTGTCATCGTCACAAGGGCTGCATGCT
479


hDUB4.8
CAACTACATGCTGTCCCGGGAGCACTCTCAAACGTGTCATCGTCACAAGGGCTGCATGCT
479


hDUB8.2
CAACTACATGCTGTCCCGGGAGCACTCTCAAACGTGTCATCGTCACAAGTGCTGCATGCT
476



************************************************* **********


 


hDUB4.5
CTGTACGATGCAAGCTCACATCACACGGGCCCTCCACAATCCTGGCCACGTCATCCAGCC
539


hDUB4.8
CTGTACGATGCAAGCTCACATCACACGGGCCCTCCACAATCCTGGCCACGTCATCCAGCC
539


hDUB8.2
CTGTACTATGCAAGCTCACATCACATGGCCCCTCCACAGTCCTGGCCATGTCATCCAGCC
536



****** ****************** ** ********* ********* ***********


 


hDUB4.5
CTCACAGGCATTGGCTGCTGGCTTCCATAGAGGCAAGCAGGAAGATGCCCATGAATTTCT
599


hDUB4.8
CTCACAGGCATTGGCTGCTGGCTTCCATAGAGGCAAGCAGGAAGATGCCCATGAATTTCT
599


hDUB8.2
CTCACAGGTGTTGGCTGCTGGCTTCCATAGAGGCGAGCAGGAAGATGCCCATGAATTTCT
596



********  ************************ *************************


 


hDUB4.5
CATGTTCACTGTGGATGCCATGAAAAAGGCATGCCTTCCCGGGCACAAGCAGGTGGATCA
659


hDUB4.8
CATGTTCACTGTGGATGCCATGAAAAAGGCATGCCTTCCCGGGCACAAGCAGGTAGATCA
659


hDUB8.2
CATGTTCACTGTGGATGCCATGAAAAAGGCATTCCTTCCCGGGCACAAGCATTTAGATAA
656



******************************** ******************  * *** *


 


hDUB4.5
TCACTCTAAGGACACCACCCTCATCCACCAAATATTTGGAGGCTACTGGAGATCTCAAAT
719


hDUB4.8
TCACTCTAAGGACACCACCCTCATCCACCAAATATTTGGAGGCTACTGGAGATCTCAAAT
719


hDUB8.2
TCACTCTAAGGACACCACCCTCATCCACCAAATATTTGGAGGGTACTGGAGATCTCACAT
716



****************************************** ************** **


 


hDUB4.5
CAAGTGTCTCCACTGCCACGGCATTTCAGACACTTTTGACCCTTACCTGGACATCGCCCT
779


hDUB4.8
CAAGTGTCTCCACTGCCACGGCATTTCAGACACTTTTGACCCTTACCTGGACATCGCCCT
779


hDUB8.2
CAACTGTTTCCACTGCCACGGGATTTCAGACACCTTTGACCCTTACCTGGACATCGCCCT
776



*** *** ************* *********** **************************


 


hDUB4.5
GGATATCCAGGCAGCTCAGAGTGTCCAGCAAGCTTTGGAACAGTTGGTGAAGCCCGAAGA
839


hDUB4.8
GGATATCCAGGCAGCTCAGAGTGTCCAGCAAGCTTTGGAACAGTTGGTGAAGCCCCAAGA
839


hDUB8.2
GGATATCCAGGCAGCTCAGAGTGTCAAGCAAGCTTTGTAACAGTTGGTGAAGCCCGAAGA
836



************************* *********** **********************


 


hDUB4.5
ACTCAATGGAGAGAATGCCTATCATTGTGGTGTTTGTCTCCAGAGGGCGCCGGCCTCCAA
899


hDUB4.8
ACTCAATGGAGAGAATGCCTATCATTGTGGTGTTTGTCTCCAGAGGGCGCCGGCCTCCAA
899


hDUB8.2
ACTCAATGGATAAAATGCCTATCATTGTGGTCTTTGTCTCCAGAAGGCGCCTGCCTCCAG
896



********** * ****************** ************ ****** *******


 


hDUB4.5
GACGTTAACTTTACACACCTCTGCCAAGGTCCTCATCCTTGTATTGAAGAGATTCTCCGA
959


hDUB4.8
GACGTTAACTTTACACACCTCTGCCAAGGTCCTCATCCTTGTATTGAAGAGATTCTCCGA
959


hDUB8.2
GACGTTAACTTTACACACTTCTGCCAAGGTCCTCATCCTTGTATTGAAGAGATTCTCTGA
956



****************** ************************************** **


 


hDUB4.5
TGTCACAGGCAACAAGATTGACAAGAATGTGCAATATCCTGAGTGCCTTGACATGAAGCT
1019


hDUB4.8
TGTGACAGGCAACAAGATTGCCAAGAATGTGCAATATCCTGAGTGCCTTGACATGCAGCC
1019


hDUB8.2
GGTCACAGGCAACAAACTTGCCAAGAATGTGCAATATCCTGAGTGCCTTGACATGCAGCC
1016



 ** ***********  *** ********************************** ***


 


hDUB4.5
ATACATGTCTCAGACGAACTCAGGACCTCTCGTCTATGTCCTCTATGCTGTGCTGGTCCA
1079


hDUB4.8
ATACATGTCTCAGCAGAACACAGGACCTCTTGTCTATGTCCTCTATGCTGTGCTGGTCCA
1079


hDUB8.2
ATACATGTCTCAGCAGAACACAGGACCTCTTGTCTATGTCCTCTATGCTGTGCTGGTCCA
1076



*************  **** ********** *****************************


 


hDUB4.5
CGCTGGGTGGAGTTGTCACAACGGACATTACTTCTCTTATGTCAAAGCTCAAGAAGGCCA
1139


hDUB4.8
CGCTGGGTGGAGTTGTCACAACGGACATTACTTCTCTTATGTCAAAGCTCAAGAAGGCCA
1139


hDUB8.2
CGCTGGGTGGAGTTGTCACAACGGACATTACTTATCTTATGTCAAA-CTCAAGAAGGCCA
1135



********************************* ************ *************


 


hDUB4.5
GTGGTATAAAATGGATGATGCCGAGGTCACCGCCTCTAGCATCACTTCTGTCCTGAGTCA
1199


hDUB4.8
ATGGTATAAAATGGATGATGCCGAGGTCACCGCCGCTAGCATCACTTCTGTCCTGAGTCA
1199


hDUP8.2
TTGGTATAAAATGGATGATGCCGAGGTCACTGCCTCCGGTATCACTTCTGTCCTGAGTCA
1195



 ***************************** *** *  * ********************


 


hDUB4.5
ACAGGCCTACGTCCTCTTTTACATCCAGAAGAGTGAATGGGAAAGACACAGTGAGAGTGT
1259


hDUB4.8
ACAGGCCTACGTCCTCTTTTACATCCAGAAGAGTGAATGGGAAAGACACAGTGAGAGTGT
1259


hDUB8.2
ACAGGCCTATGTCCTCTTTTACATCCAGAAGAATGAATTTGGAAGACCCAGTTACAGTGT
1255



********* ********************** *****  * ***** **** * *****


 


hDUB4.5
GTCAAGAGGCAGGGAACCAAGAGCCCTTGGCGCAGAAGACACAGACAGGCGAGCAACGCA
1319


hDUB4.8
GTCAAGAGGCAGGGAACCAAGAGCCCTTGGCGCAGAAGACACAGACAGGCGAGCAACGCA
1319


hDUB8.2
GTCCATAGGCAGGCAACCAAGAGCTCTTTGCGTGAAGGCAAGTGAATTGTGTGTGAAATA
1315



*** * ****************** *** ***   * *  *  **   * * *  *   *


 


hDUB4.5
AGGAGAGCTCAAGAGAGACCACCCCTGCCTCCAGGCCCCCGAGTTGGACGAGCACTTGGT
1379


hDUB4.8
AGGAGAGCTCAAGAGAGACCACCCCTGCCTCCAGGCCCCCGAGTTGGACGAGCACTTGGT
1379


hDUB8.2
AAATG---TCATGA---ATAAATCTTGCAGTGGAGTATTT-ATTTGTCTCACTTTGTAAT
1368



*   *   *** **   *  *  * ***      *      * ***    *     *  *


 


hDUB4.5
GGAAAGAGCCACTCAGGAAAGCACCTTAGACCACTGGAAATTCCTTCAAGAGCAAAACAA
1439


hDUB4.8
GGAAAGAGCCACTCAGGAAAGCACCTTAGACCACTGGAAATTCCTTCAAGAGCAAAACAA
1439


hDUB8.2
CAGTGAATGAGCTTTAACCAATATCAATGCCTAGTGCCTACCCCCCAGAGATAAGAACTT
1428



      *    **      *  * *   * * * **   *  **    ***  * ***


 


hDUB4.5
AACGAAGCCTGAGTTCAACGTCAGAAAAGTCGAAGGTACCCTGCCTCCCGACGTACTTGT
1499


hDUB4.8
AACGAAGCCTGAGTTCAACGTCAGAAAAGTCGAAGGTACCCTGCCTCCCGACGTACTTGT
1499


hDUB8.2
CCACTCTCTTATGTGTAAC--CATGGCCTCTGGATTGCTTATGACTCTGAAGATAATTCT
1486



       * *  **  ***  **        * *       ** ***   *  ** ** *


 


hDUB4.5
GATTCATCAATCAAAATACAAGTGTGGGATGAAGAACCATCATCCTG-AACAGCAAAGCT
1558


hDUB4.8
GATTCATCAATCAAAATACAAGTGTGGGATGAAGAACCATCATCCTG-AACAGCAAAGCT
1558


hDUB8.2
CCTT--TCCCCCAACGTTTCAGAATCACTTCAGGTGGTGGTAACAGATAACACATCAGTC
1544



  **  **   ***  *   **  *    * * *       * *    ****    **


 


hDUB4.5
CCCTGCTAAACCTCTCTTCGACGACCCCGACACATCAGGAGTCCATGAACACTGGCACAC
1618


hDUB4.8
CCCTGCTAAACCTCTCTTCGTCGACCCCGACACATCAGGAGTCCATGAACACTGGCACAC
1618


hDUB8.2
CCTTTCTCTCTCTTTTCTCTTCACTCAGGAAAACTCTCACTGAGACAAAGGAAAATCCTA
1604



** * **   ** *  **  *   *  ** *  **        *  **       *


 


hDUB4.5
TCGCTTCCCTGCGAGGGAGGGC-----CAGGAGATCCAAAGGGAAGAACAAACACAGCAA
1673


hDUB4.8
TCGCTTCCCTGCGAGGGAGGGC-----CAGGAGATCCAAAGGGAAGAACAAACACAGCAA
1673


hDUB8.2
TGGTTTACTGGGGAGGAAGAATTCCCTCAGGAGTGAAATTGGTGGCTCCTTCCTCCCTGT
1664



* * ** *  * **** **        ******    *  **      *   * *


 


hDUB4.5
GAGGGCTCTGCTTGTGTG----CCAGTGGTCTCAGTGGAAGTACCGACCCACA 1722


hDUB4.8
GAGGGCTCTGCTTGTGTG----CCAGTGA------------------------ 1698


hDUB8.2
CAAGTCTCTTCCTCAGGATTGCCCCTTTGTCTCTTCAGGACT----------- 1706



 * * **** * *  *      **  *

















TABLE 26





Deduced amino acid alignment of hDUB4.5 (Seq ID NO. 14),



hDUB4.8 (Seq ID NO. 20) and hDUB8.2 (Seq ID NO. 44).


N-terminal potential mitochondrial targeting sequences are underlined.


















hDUB4.5
MRQRARHLKTLSEGIASFCNLRSQQKNLVILVPVDMEEDSLYLGGEWQFNHFSKLTSSRP
60



hDUB4.8
MRQRARHLKTLSEGIASCCKLRSQQKNLVILVPVDMEDDSLYLGGEWQFNHFSKLTSSRP
60


hDUB8.2
MRPESPSFED-SEEIASFCNLRSQPKNLVILVPGDMEDDSLYLGGEWQFNHFSKLTSSRP
59



** .:  ::  ** *** *:**** ******** ***:**********************


 


hDUB4.5
DAAFAEIQRTSLPEKSPLSCETRVDLCDDLAPVARQLAPREKLPLSNRRPAAVGAGLQNM
120


hDUB4.8
DAAFAEIQRTSLPEKSPLSCETRVDLCDDLAPVARQLAPREKLPLSSRRPAAVGAGLQNM
120


hDUB8.2
DAAFAEIQRTSLSEKSSLSSETRVDLCDDLAPVARQLAPREKLPLSSRRPAAVGAGLQNM
119



************.***.**.**************************.*************


 


hDUB4.5
GNTCYVNASLQCLTYTPPLANYMLSREHSQTCHRHKGCMLCTMQAHITRALHNPGHVIQP
180


hDUB4.8
GNTCYVNASLQCLTYTPPLANYMLSREHSQTCHRHKGCMLCTMQAHITRALHNPGHVIQP
180


hDUB8.2
GNTCYVNASLQCLTYTPPLANYMLSREHSQTCHRHKCCMLCTMQAHITWPLHSPGHVIQP
179



************************************ *********** .**.*******


 


hDUB4.5
SQALAAGFHRGKQEDAHEFLMFTVDAMKKACLPGHKQVDHHSKDTTLIHQIFGGYWRSQI
240


hDUB4.8
SQALAAGFHRGKQEDAHEFLMFTVDAMKKACLPGHKQVDHHSKDTTLIHQIFGGYWRSQI
240


hDUB8.2
SQVLAAGFHRGEQEDAHEFLMFTVDAMKKAFLPGHKHLDNHSKDTTLIHQIFGGYWRSHI
239



**.********:****************** *****::*:******************:*


 


hDUB4.5
KCLHCHGISDTFDPYLDIALDIQAAQSVQQALEQLVKPEELNGENAYHCGVCLQRAPASK
300


hDUB4.8
KCLHCHGISDTFDPYLDIALDIQAAQSVQQALEQLVKPEELNGENAYHCGVCLQRAPASK
300


hDUB8.2
NCFHCHGISDTFDPYLDIALDIQAAQSVKQAL----------------------------
271



:*:*************************:***


 


hDUB4.5
TLTLHTSAKVLILVLKRFSDVTGNKIDKNVQYPECLDMKLYMSQTNSGPLVYVLYAVLVH
360


hDUB4.8
TLTLHTSAKVLILVLKRFSDVTGNKIAKNVQYPECLDMQPYMSQQNTGPLVYVLYAVLVH
360


hDUB8.2
------------------------------------------------------------


 


hDUB4.5
AGWSCHNGHYFSYVKAQEGQWYKMDDAEVTASSITSVLSQQAYVLFYIQKSEWERHSESV
420


hDUB4.8
AGWSCHNGHYFSYVKAQEGQWYKMDDAEVTAASITSVLSQQAYVLFYIQKSEWERHSESV
420


hDUB8.2
------------------------------------------------------------


 


hDUB4.5
SRGREPRALGAEDTDRRATQGELKRDHPCLQAPELDEHLVERATQESTLDHWKFLQEQNK
480


hDUB4.8
SRGREPRALGAEDTDRRATQGELKRDHPCLQAPELDEHLVERATQESTLDHWKFLQEQNK
480


hDUB8.2
------------------------------------------------------------


 


hDUB4.5
TKPEFNVRKVEGTLPPDVLVIHQSKYKCGMKNHHPEQQSSLLNLSSTTPTHQESMNTGTL
540


hDUB4.8
TKPEFNVRKVEGTLPFDVLVIHQSKYKCGMKNHHPEQQSSLLNLSSSTPTHQESMNTGTL
540


hDUB8.2
------------------------------------------------------------


 


hDUB4.5
ASLRGRARRSKGKNKHSKRALLVCQWSQWKYRPT 574


hDUB4.8
ASLRGRARRSKGKNKHSKRALLVCQ--------- 565


hDUB8.2
----------------------------------

















TABLE 27





Upstream of initiation codon nucleotide sequence



(putative promoter region) alignment of


hDUB4.5 (Seq ID NO. 13), hDUB4.8 (Seq ID NO. 19)


and hDUB8.2 (Seq ID NO. 43).


Numbering is initiated from initiation ATG.


















hDUB4.5
CACACGAACACAATCACACACACACACTCACACGGTTTCCTACGTAAAGATTTCTTCCCT
−276



hDUB4.8
CACACGAACACAATCACACACACACACTCACACGGTTTCCTACGTAAAGATTTCTTCCCT
−276


hDUB8.2
GGGAGAAAAACACACACACACACACACACACACGGTTTCATAGGTAAAGATTTCTTCCCT
−276



   *  ** ***  ************* *********** ** *****************


 


hDUB4.5
GCCATTGCTTTACCTAAAATAAGGCAACTGTGTGGCCACTGTCCCAACCCGGTTACACTC
−216


hDUB4.8
GCCATTGCTTTACCTAAAATAAGGCAACTGTGTGGCCACTGTCCCAACCCGGTTACACTC
−216


hDUB8.2
GACATTGTTTTACCTAAAATAAGGCAACTGTGTGGCCACTGTCCCAACCCGGTTACACTC
−216



* ***** ****************************************************


 


hDUB4.5
CTATTATATGTGCCTATCATCCTGAGGAGTAATTTGATTCAGGTGTTCTGGAAGTCATGC
−156


hDUB4.8
CTATTATATGTGCCTATCATCCTGAGGAGTAATTTGATTCAGGTGTTCTGGAAGTCATGC
−156


hDUB8.2
ATATTACATGTGTCTATCAGCCTGAGGAGTAGTTTGATTCAGGTGTTCTAGAAGTCATGA
−156



  ***** ***** ****** *********** ***************** *********


 


hDUB4.5
TGTGGGCTGTGTCTGTTGAATTCCCAGCGATGCAAGGGGACACACCCTGTGACTCCTTCC
−96


hDUB4.8
TGTGGGCTGTGTCTGTTGAATACCCAGCGATGCAAGGGGACACACCCTGTGACTCCTTCC
−96


hDUB8.2
TGTGGCCTGTGTCTGTTGAATTCCCAGCGATGCAAGGGGACACACCCTGTGACTCATTCC
−96



********************* ********************************* ****


 


hDUB4.5
TGAATTGAGTGCTGATATTTGATTGGCTTATCGCGCACCTGATGAGTGAGTGGGGTGTTC
−36


hDUB4.8
TGAATTGAGTGCTGATATTTGATTGGCTTATCGCGCACCTGATGAGTGAGTGGGGTGTTC
−36


hDUB8.2
TTAATTGAGTGCTGATATTTGATTGGTTTATCGCGCACCTGATGGGTGGGTGGGGTGTTC
−36



* ************************ ********************* ***********


 


hDUB4.5
GCGGTTGGTGGGGTTGACTTACAGAAGGGCTGATG 0


hDUB4.8
GCGGTTGGTGGGGGTGACTTACAGAAGGGCTGATG 0


hDUB8.2
GCGGTTGGTGGGGGTGAGTTATATAAGGGCTGATG 0



************* *** *** * ***********

















TABLE 28





CLUSTAL W (1.81) multiple sequence alignment



of core amino acids of hDUBs (8.5: Seq ID NO. 30; 8.7: Seq


ID NO. 34; 8.1: Seq ID NO. 26; 4.2: Seq ID NO. 10; 4.3: Seq


ID NO. 12; 4.5: Seq ID NO. 14; 4.1: Seq ID NO. 6; 8.3: Seq


ID NO. 28; 8.11: Seq ID NO. 38; 8.8: Seq ID NO. 36;


8.6: Seq ID NO. 32).


















8.5
MEDDSLYLGGEWQFNHFSKLTSSRPDAAFAEIQRTSLPEKSPLSSEARVDLCDDLAPVAR
60



8.7
MEDDSLYLGGEWQFNHFSKLTSSRPDAAFAEIQRTSLPEKSPLSSEARVDLCDDLAPVAR
60


8.1
MGDDSLYLGGEWQFNHFSKLTSSRPDAAFAEIQRTSLPEKSPLSSETRVDLCDDLAPVAR
60


4.2
MEDDSLYLGGEWQFNHFSKLTSSRPDAAFAEIQRTSLPEKSPLSCETRVDLCDDLAPVAR
60


4.3
MEDDSLYLGGEWQFNHFSKLTSSRPDAAFAEIQRTSLPEKSPLSCETRVDLCDDLAPVAR
60


4.5
MEEDSLYLGGEWQFNHFSKLTSSRPDAAFAEIQRTSLPEKSPLSCETRVDLCDDLAPVAR
60


4.1
MEDDSLYLGGEWQFNHFSKLTSSRPDAAFAEIQRTSLPEKSPLSCETRVDLCDDLAPVAR
60


8.3
MEDDSLYLGGEWQFNHFSKLTSSRPDAAFAEIQRTSLPEKSQLSTETRVDFCDDLAPVAR
60


8.11
MEDDSLYLGGEWQFNHFSKLTSSRPDAAFAEIQRTSLPEKSQLSTETRVDFCDDLAAVAR
60


8.8
MEDDSLYLGGDWQFNHFSKLTSSRLDAAFAEIQRTSLSEKSPLSSETRFDLCDDLAPVAR
60


8.6
MEDDSLYLGGDWQFNHFSKLTSSRLDAAFAEIQRTSLSEKSPLSSETRFDLCDDLAPVAR
60



* :*******:************* ************.*** ** *:*.*:*****.***


 


8.5
QLAPRKKLPLSSRRPAAVGAGLQNMGNTCYENASLQCLTYTPPLANYMLSREHSQTCQRP
120


8.7
QLAPRKKLPLSSRRPAAVGAGLQNMGNTCYENASLQCLTYTPPLANYMLSREHSQTCQRP
120


8.1
QLAPREKLPLSSRRPAAVGAGLQNMGNTCYENASLQCLTYTLPLANYMLSREHSQTCQRP
120


4.2
QLAPREKLPLSSRRPAAVGAGLQNMGNTCYVNASLQCLTYTTPLANYMLSREHSQTCHRH
120


4.3
QLAPREKLPLSSRRPAAVGAGLQNMGNTCYVNASLQCLTYTPPLANYMLSREHSQTCHRH
120


4.5
QLAPREKLPLSNRRPAAVGAGLQNMGNTCYVNASLQCLTYTPPLANYMLSREHSQTCHRH
120


4.1
QLAPREKPPLSSRRPAAVGAGLQNMGNTCYVNASLQCLTYKPPLANYMLFREHSQTCHRH
120


8.3
QLAPREKLPLSSRRPAAVGAGLQNMGNTCYVNASQQCLTYTPPLANYMLSREHSQTCHRH
120


8.11
QLAPREKLPLSSRRPAAVGAGLQNMGNTCYVNASQQCLTYIPPLANYMLSREHSQTCHRH
120


8.8
QLAPREKLPLSSRRPAAVGAGLQKIGNTFYVNVSLQCLTYTLPLSNYMLSREDSQTCHLH
120


8.6
QLAPREKLPLSSRRPAAVGAGLQKIGNTFYVNVSLQCLTYTLPLSNYMLSREDSQTCHLH
120



*****:* ***.***********::*** * *.* *****  **:**** **.****:


 


8.5
KCCMLCTMQAHITWALHSPGHVIQPSQALAAGFHRGKQEDAHEFLMFTVDAMKKACLPGH
180


8.7
KCCMLCTMQAHITWALHSPGHVIQPSQALAAGFHRGKQEDAHEFLMFTVDAMKKACLPGH
180


8.1
KCCMLCTMQAHITWALHSPGHVIQPSQALAAGFHRGKQEDVHEFLMFTVDAMKKACLPGH
180


4.2
KGCMLCTMQAHITRALHNPGHVIQPSQALAAGFHRGKQEDAHEFLMFTVDAMKKACLPGH
180


4.3
KGCMLCTMQAHITRALHNPGHVIQPSQALAAGFHRGKQEDAHEFLMFTVDAMKKACLPGH
180


4.5
KGCMLCTMQAHITRALHNPGHVIQPSQALAAGFHRGKQEDAHEFLMFTVDAMKKACLPGH
180


4.1
KGCMLCTMQAHITRALHIPGHVIQPSQALAAGFHRGKQEDAHEFLMFTVDAMRKACLPGH
180


8.3
KCCMLCTMEAHITWPLHIPGHVIQPSQALAAGFHRGKQEAALEFLMFTVDAMKKACLPGH
180


8.11
KCCMLCTMEAHITWPLHIPGHVIQPSQALAAGFHRGKQEAALEFLMFTVDAMKKACLPGH
180


8.8
KCCMFCTMQAHITWALYRPGHVIQPSQVLAAGFHRGEQEDAHEFLMFTVDAMKKACLPGH
180


8.6
KCCMFCTMQAHITWALYRPGHVIQPSQVLAAGFHRGEQEDAHEFLMFTVDAMKKACLPGH
180



* **:***:**** .*: *********.********:** . **********:*******


 


8.5
KQVDHHSKDTTLIHQIFGGCWRSQIKCLHCHGISDTFDPYLDIALDIQAAQSVKQALEQL
240


8.7
KQVDHHSKDTTLIHQIFGGCWRSQIKCLHCHGISDTFDPYLDIALDIQAAQSVKQALEQL
240


8.1
KQVDHHCKDTTLIHQIFGGCWRSQIKCLHCHGISDTFDPYLDIALDIQAAQSVKQALEQL
240


4.2
KQVDHHSKDTTLIHQIFGGYWRSQIKCLHCHGISDTFDPYLDIALDIQAAQSVQQALEQL
240


4.3
KQVDHHSKDTTLIHQIFGGYWRSQIKCLHCHGISDTFDPYLDIALDIQAAQSVQQALEQL
240


4.5
KQVDHHSKDTTLIHQIFGGYWRSQIKCLHCHGISDTFDPYLDIALDIQAAQSVQQALEQL
240


4.1
KQVDRHSKDTTLIHQIFGGYWRSQIKCLHCHGISDTFDPYLDIALDIQAAQSVQQALEQL
240


8.3
KQVDHHSKDTTLIHQIFGGYWRSQIKCLHCHGISDTFGPYLDIALDIQEAQSVKQALEQL
240


8.11
K----------------------QILILVWKRFSDVTG----------------------
196


8.8
KQLDHHSKDTTLIHQIFGAYWRSQIKYLHCHGISDTFDPYLDIALDIQAAQSVKQALEQL
240


8.6
KQLDHHSKDTTLIHQIFGAYWRSQIKYLHCHGISDTFDPYLDIALDIQAAQSVKQALEQL
240



*                      **  *  : :**. .


 


8.5
VKPEELNGENAYHCGLCLQRAPVSKTLTLHTFAKERILETQRPWVVTRHKLAKSVQYAES
300


8.7
VKPEELNGENAYHCGLCLQRAPASKTLTLHTSAKVLILVLKRFSDVTGNKLAKNVQYPEC
300


8.1
VKPEELNGENAYHCGLCLQRAPASNTLTLHTSAKVLILVLKRFSDVAGNKLAKNVQYPEC
300


4.2
VKPEELNGENAYHSGVCLQRAPASKTLTLHTSAKVLILVLKRFSDVTGNKIAKNVQYPEC
300


4.3
VKPEELNGENAYHCGVCLQRAPASKTLTLHTSAKVLILVLKRFSDVTGNKIAKNVQYPEC
300


4.5
VKPEELNGENAYHCGVCLQRAPASKTLTLHTSAKVLILVLKRFSDVTGNKIDKNVQYPEC
300


4.1
VKPEELNGENAYHCGVCLQRAPASKTLTLHNSAKVLILVLKRFPDVTGNKIAKNVQYPEC
300


8.3
VKPEELNGENAYHC---------------------------------GNKIAKNVQYPEC
267


8.11
------------------------------------------------NKIAKNVQYPEC
208


8.8
VKPKELNGENAYHCGLCLQKAPASKTLTLPTSAKVLILVLKRFSDVTGNKLAKNVQYPKC
300


8.6
VKPKELNGENAYHCGLCLQKAPASKTLTLPTSAKVLILVLKRFSDVTGNKLAKNVQYPKC
300



                                                :*: *.***.:.


 


8.5
LDMQPYMSQQNTGPLVYVLYAVLVHAGWSCHDGHYFSYVKAQEGQWYKMDDAKVTACSIT
360


8.7
LDMQPYMSQQNTGPLVYVLYAVLVHAGWSCHDGHYFSYVKAQEGQWYKMDDAKVTACSIT
360


8.1
LDMQPYMSQQNTGPLVYVLYAVLVHAGWSCHDGHYFSYVKAQEVQWYKMDDAEVTVCSII
360


4.2
LDMQPYMSQQNTGPLVYVLYAVLVHAGWSCHNGHYFSYVKAQEGQWYKMDDAEVTAASIT
360


4.3
LDMQPYMSQQNTGPLVYVLYAVLVHAGWSCHNGHYFSYVKAQEGQWYKMDDAEVTAASIT
360


4.5
LDMKLYMSQTNSGPLVYVLYAVLVHAGWSCHNGHYFSYVKAQEGQWYKMDDAEVTASSIT
360


4.1
LDMQPYMSQQNTGPLVYVLYAVLVHAGWSCHNGHYSSYVKAQEGQWYKMDDAEVTASSIT
360


8.3
LDMQPYMSQQNTGPLVYVLYAVLVHAGWSCHNGHYFSYVKVQEGQWYKMDDAEVTASGIT
327


8.11
LDMQPYMSQQNTGPLVYVLYAVLVHAGWSCHNGHYFSYVKVQEGQWYKMDDAE-------
261


8.8
RDMQPYMSQQNTGPLVYVLYAVLVHAGWSCHNGHYFSYVKAQEGQWYKMDDAEVTASGIT
360


8.6
RDMQPYMSQQNTGPLVYVLYAVLVHAGWSCHNGHYFSYVKAQEGQWYKMDDAEVTASGIT
360



 **: **** *:*******************:*** ****.** ********:


 


8.5
SVLSQQAYVLFYIQKSEWERHSESVSRGREPRALGAEDTDRRATQGELKRDHPCLQAPEL
420


8.7
SVLSQQAYVLFYIQKSEWERHSESVSRGREPRALGAEDTDRRATQGELKRDHPCLQAPEL
420


8.1
SVLSQQAYVLFYIQKSEWERHSESVSRGREPRALGAEDTDRRAKQGELKRDHPCLQAPEL
420


4.2
SALSQQAYVLFYIQKSEWERHSESVSRGREPRALGTEDTDRRATQGELKRDHPCLQAPEL
420


4.3
SVLSQQAYVLFYIQKSEWERHSESVSRGREPRALGAEDTDRRATQGELKRDHPCLQAPEL
420


4.5
SVLSQQAYVLFYIQKSEWERHSESVSRGREPRALGAEDTDRRATQGELKRDHPCLQAPEL
420


4.1
SVLSQQAYVLFYIQKSEWERHSESVSRGREPRALGVEDTDRRATQGELKRDHPCLQAPEL
420


8.3
SVLSQQAYVLFYIHKSEWERHSESVSRGREPRALGAEDTDRRATQGELKRDYPCLQVPEL
387


8.11
--------------KSEWERHSESVSRGREPRALGAEDTDRRATQGELKRDYPCLQVPEL
307


8.8
SVLSQQAYVLFYIQKSEWERHSESVSRGREPRALGAEDTDRPATQGELKRDHPCLQVPEL
420


8.6
SVLSQQAYVLFYIQKSEWERHSESVSRGREPRALGAEDTDRPATQGELKRDHPCLQVPEL
420



              *********************.***** *.*******:****.***


 


8.5
DERLVERATQESTLDHWRFPQEQNKTKPEFNVRKVEGTLPPNVLVIHQSKYKCGMKNHHP
480


8.7
DERLVERATQESTLDHWRFPQEQNKTKPEFNVRKVEGTLPPNVLVIHQSKYKCGMKNHHP
480


8.1
DEHLVERATQESTLDHWKFLQEQNKTKPEFNVGKVEGTLPPNALVIHQSKYKCGMKNHHP
480


4.2
DEHLVERATQESTLDHWKFLQEQNKTKPEFNVRKVEGTLPPDVLVIHQSKYKCGMKNHHP
480


4.3
DEHLVERATQESTLDRWKFLQEQNKTKPEFNVRKVEGTLPPDVLVIHQSKYKCGMKNHHP
480


4.5
DEHLVERATQESTLDHWKFLQEQNKTKPEFNVRKVEGTLPPDVLVIHQSKYKCGMKNHHP
480


4.1
DEHLVERATQESTLDHWKFLQEQNKTKPEFNVRRVEGTVPPDVLVIHQSKYKCRMKNHHP
480


8.3
DEHLVERATQESTLDHWKFLQEQNKTKPEFNVRKLEGTLPPNVLVIHQSKYKCGMKNHHP
447


8.11
DEHLVERATQESTLDHWKFLQEQNKTKPEFNVRKLEGTLPPNVLVIHQSKYKCGMKNHHP
367


8.8
DEHLVERATQESTLDHWKFPQKQNKTKPEFNVRKVEGTLPPNVLVIHQSKYKCGMKNHHP
480


8.6
DEHLVERATQESTLDHWKFPQKQNKTKPEFNVRKVEGTLPPNVLVIHQSKYKCGMKNHHP
480



**:************:*:* *:********** ::***:**:.********** ******


 


8.5
EQQSSLLNLSSTTRTDQESVNTGTLASLQGRTRRSKGKNKHSKRALLVCQ 530


8.7
EQQSSLLNLSSTTRTDQESVNTGTLASLQGRTRRSKGKNKHSKRALLVCQ 530


8.1
EQQSSLLNLSSTTRTDQESMNTGTLASLQGRTRRAKGKNKHSKRALLVCQ 530


4.2
EQQSSLLNLSSSTPTHQESMNTGTLASLRGRARRSKGKNKHSKRALLVCQ 530


4.3
EQQSSLLNLSSSTPTHQESMNTGTLASLRGRARRSKGKNKHSKRALLVCQ 530


4.5
EQQSSLLNLSSTTPTHQESMNTGTLASLRGRARRSKGKNKHSKRALLVCQ 530


4.1
EQQSSLLNLSSTTPTDQESMNTGTLASLRGRTRRSKGKNKHSKRALLVCQ 530


8.3
EQQSSLLNLSSTNPTDQESMNTGTLASLQGRTRRAKGKNKHCKRALLVCQ 497


8.11
EQQSSLLNLSSTNPTDQESMNTGTLASLQGRTRRSKGKNKHCKRALLVCQ 417


8.8
EQQSSVLNLSSTKPTDQESMNTGTLASLQGSTRRSKGNNKHSKRSLLVCQ 530


8.6
EQQSSLLNLSSTKPTDQESMNTGTLASLQGSTRRSKGNNKHSKRSLLVCQ 530



*****:*****:. *.***:********:* :**:**:***.**:*****

## Claims

1. An isolated polypeptide comprising the human deubiquitinating protease hDUB4.1b (SEQ ID NO: 6).