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TATA Box (0):
Recent article
TATA Box
Genetika (Moskva) (46)4 2010
Abstract
Most of more than 11 million experimentally established polymorphisms, accumulated in dbSNP, were identified in the intergenic spacers or coding DNA regions. This fact enables interpretation of the former polymorphisms as neutral, while the latter make clear the biological sense of the associated mu...
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PMID: 20536014
PDF is available here.
PDF is available here.
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Abstract
We have considered an ensemble of configurations from crystallographic data of the TBP-TATA box complex structures under a given thermodynamic condition. Analysis of the ensemble of structures of this complex indicates that the DNA deforms significantly to form specific hydrogen bonds and as a conse...
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PMID: 19916565
PDF is available here.
PDF is available here.
BMC Genomics (11) 2010
Abstract
We reexamined the spatial distribution of TFBSs, investigated various promoter features that may affect the distribution, and studied the effect of TFBS distribution on transcriptional regulation.
We found a sharp peak for the distribution of TFBSs at ~115 bp upstream of the TSS, but no clear peak w...
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PMID: 20958978
PDF is available here.
PDF is available here.
Abstract
We have analyzed 69 experimental datasets on the characteristics of biologicacally important features altered by TATA-box mutations. Among these features, the TBP/TATA-complex parameters, the transcription level, the activity of gene products, yeast colony growth at a dose of growth inhibitor (pheno...
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PMID: 20586319
PDF is available here.
PDF is available here.
Abstract
Among 2261 samples, 125 showed high level of HbA2 and were diagnosed as beta-Thalassemia (5.53%). Genotypes of the patients were classified as: 59 cases with beta-globin gene condon (CD) 41-42 mutation, 33 cases CD17 mutation, 18 cases with TA TA box nt-28 mutation, 7 with IVS-II-654 mutation, 3 wit...
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PMID: 20193381
PDF is available here.
PDF is available here.
Cancer Biology & Therapy (8)10 2009
Abstract
We investigated the mechanism by which retinoic acid induces the expression of the human tumor suppressor GPRC5A. The proximal 5' upstream region of the GPRC5A gene was found to contain two potential RAR/RXR binding sites (RAREs) and one VDR/RXR binding site with direct repeat 5 (DR5) motifs designa...
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PMID: 19279407
PDF is available here.
PDF is available here.
Abstract
We present a first genome-wide computational analysis of the TATA box and Y Patch distribution in rice (Oryza sativa L. subsp. japonica) promoter sequences. Utilizing a probabilistic sequence model, we ascertain that only approximately 19% of rice genes possess the TATA box, but approximately 50% co...
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PMID: 19234558
PDF is available here.
PDF is available here.
Biochemistry (New York) (74)2 2009
Abstract
TATA-binding protein (TBP) is the first basal factor that recognizes and binds a TATA box on TATA-containing gene promoters transcribed by RNA polymerase II. Data available in the literature are indicative of admissible variability of the TATA box. The TATA box flanking sequences can influence TBP a...
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PMID: 19267666
PDF is available here.
PDF is available here.
Journal of Immunology (182)2 2009
Abstract
We show that in contrast to T cells, peripheral blood NK cells express CCL5 constitutively. The use of specific inhibitors of the JNK, ERK, and p38 MAPK pathways showed that the JNK pathway controls expression of CCL5 by NK cells. Promoter-reporter assays identified a compact region of the CCL5 prom...
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PMID: 19124744
PDF is available here.
PDF is available here.
Abstract
Successive 5' deletions progressively lowered fold-induction by activin A from 9.5 to zero, but progressively increased basal expression. Replacing deletions with substitute DNA showed no changes in basal expression or fold-induction. Induction by activin A was supported by the minimal rat prolactin...
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PMID: 19552818
PDF is available here.
PDF is available here.
BMC Plant Biology (9)1 2009
Abstract
We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP) gene promoters from three plant families, namely Brassicaceae (mustards), Fabaceae (legumes) and Poaceae (grasses) using backgrounds based on complete sets of promoters from...
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PMID: 19843335
PDF is available here.
PDF is available here.
Journal of Dental Research (87)12 2008
Abstract
We previously showed that methyl methacrylate (MMA) induced mRNA expression of the glutathione S-transferase alpha 1 gene (Gsta1) located downstream of the cis-acting anti-oxidant responsive element (ARE). Herein, we tested the hypothesis that MMA activated the Gsta1 promoter through the ARE. HepG2...
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PMID: 19029078
PDF is available here.
PDF is available here.
Journal of Virology (82)21 2008
Abstract
We report an initial characterization of the E1 cistron of HPV type 16 (HPV-16), the most common oncogenic mucosal HPV type found in cervical and some head and neck cancers. The first step in HPV DNA replication is an initial burst of plasmid viral DNA amplification. Complementation assays between H...
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PMID: 18753208
PDF is available here.
PDF is available here.
Journal of General Virology (89)Pt 11 2008
Abstract
The human T-cell leukemia virus type 1 (HTLV-1) Tax oncoprotein transforms human lymphocytes and is critical for the pathogenesis of HTLV-1-induced adult T-cell leukaemia. In HTLV-transformed cells, Tax upregulates interleukin (IL)-13, a cytokine with proliferative and anti-apoptotic functions that...
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PMID: 18931077
PDF is available here.
PDF is available here.
Genes & Development (22)20 2008
Abstract
We explored potential biological functions of the DPE. We found that nearly all of the Drosophila homeotic (Hox) gene promoters, which lack TATA-box elements, contain functionally important DPE motifs that are conserved from Drosophila melanogaster to Drosophila virilis. We then discovered that Caud...
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PMID: 18923080
PDF is available here.
PDF is available here.
Collegium Antropologicum (32)3 2008
Abstract
Increased serum bilirubin levels in patients with Gilbert syndrome (GS) are caused by reduction of hepatic activity of bilirubin glucuronosyltranferase to about 30% of normal. UGT1A1 genetic polymorphism with absent or very low bilirubin UDP-glucuronosyltransferase (B-UGT) activity is associated wit...
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PMID: 18982743
PDF is available here.
PDF is available here.
Genes & Development (22)17 2008
Abstract
The RNA polymerase II core promoter is a structurally and functionally diverse transcriptional module. RNAi depletion and overexpression experiments revealed a genetic circuit that controls the balance of transcription from two core promoter motifs, the TATA box and the downstream core promoter elem...
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PMID: 18703680
PDF is available here.
PDF is available here.
Abstract
UDP glucuronosyltransferases (UGTs) play an important role for drug detoxification and toxicity. UGT function is genetically modulated by single nucleotide polymorphisms (SNPs) which lead to the expression of functionally altered protein, or altered expression levels. UGT1A4 activity includes antico...
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PMID: 18433817
PDF is available here.
PDF is available here.
Abstract
Genes and Immunity (9)7 2008
Abstract
We show that active and silent chromatin modifications characterize the regulatory regions of IL-1alpha in expressing and non-expressing cells, respectively, and that the DNA methylation in the proximal promoter is associated with the expression status of the cells. Interestingly, although nucleosom...
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PMID: 18615092
PDF is available here.
PDF is available here.
Abstract
We demonstrate the differential expression of the HSP90 isoforms, HSP90alpha and beta, in rat gliosarcoma 9L cells using a modified SDS-PAGE system that allowed us to distinguish the isoforms. We subsequently assessed the transcriptional controls involving the transcription elements located in the p...
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PMID: 18320580
PDF is available here.
PDF is available here.
Abstract
We describe the rational design of minimal hypoxia-inducible enhancers, conceptually equivalent to using an optimized HIF-binding site (HBS) as the building block. Optimizations of the HBS, spacing between HBSs, the distance from the minimal promoter, and orientation of HBSs allowed us to design con...
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PMID: 18402769
PDF is available here.
PDF is available here.
Abstract
The crystal structure of a complex between the bimolecular human telomeric quadruplex d(TAGGGTTAGGGT)2 and the experimental anticancer drug BRACO-19, has been determined, to 2.5 A resolution. The binding site for the BRACO-19 molecule is at the interface of two parallel-folded quadruplexes, sandwich...
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PMID: 18457389
PDF is available here.
PDF is available here.
Abstract
These results indicate the potential of this novel poxvirus promoter for driving high levels of gene expression....
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PMID: 18535635
PDF is available here.
PDF is available here.
Abstract
The RNA polymerase II core promoter is generally defined to be the sequence that directs the initiation of transcription. This simple definition belies a diverse and complex transcriptional module. There are two major types of core promoters - focused and dispersed. Focused promoters contain either...
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PMID: 18436437
PDF is available here.
PDF is available here.
Abstract
We show by footprinting with DNase I and permanganate that nearly all sequences between the enhancer-like distal sequence element and the initiation site are protected during interphase whereas the upstream half of the U2 snRNA coding region is exposed. We also show by chromatin immunoprecipitation...
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PMID: 18378697
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1779)5 2008
Abstract
We present evidence that GAGA factor enhances transcription by stabilizing pre-initiation complex (PIC) and promoting reinitiation. Formation of PIC prior to GAGA addition prevents activation suggesting that GAGA is required early in the formation of activated complexes. GAGA stimulation of transcri...
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PMID: 18394434
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)9 2008
Abstract
We performed transcription reactions using highly purified proteins and CYC1 promoter TATA box mutants. The TATA box consensus sequence is a good predictor of promoter activity. However, several nonconsensus sequences are almost fully functional, indicating that mechanistic requirements are not the...
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PMID: 18385157
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)9 2008
Abstract
We report a comprehensive investigation of the regulatory mechanism of a heat-induced gene (hsp5) from Halobacterium salinarum. We demonstrated by mutation analysis that the sequences 5' and 3' to the core elements (TATA box and BRE) of the hsp5 promoter (P(hsp5)) did not significantly affect the ba...
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PMID: 18390887
PDF is available here.
PDF is available here.
Journal of Virology (82)7 2008
Abstract
We have recently shown that ICP4 has a differential requirement for the general transcription factor TFIIA in vitro (S. Zabierowski and N. DeLuca, J. Virol. 78:6162-6170, 2004). TFIIA was dispensable for ICP4 activation of a late promoter (gC) but was required for the efficient activation of an earl...
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PMID: 18216093
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)12 2008
Abstract
We investigated the mechanism of regulated elongation of c-myc and human immunodeficiency virus-1 (HIV-1) using an in vitro elongation assay that reproduces the conditional block to elongation. We found that HIV-1 Tat can activate the RNAPII transcription complexes paused on c-myc by enhancing their...
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PMID: 18218627
PDF is available here.
PDF is available here.
Abstract
We show that the 504-bp 5' upstream sequence is the shortest promoter directing reporter activities in all Crz neurons. Further dissection of this sequence revealed two important regions responsible for group specificity: -504::-419 for DM expression and -380::-241 for DL and vCrz expression. The la...
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PMID: 18181151
PDF is available here.
PDF is available here.
Journal of Gene Medicine (10)3 2008
Abstract
Of the 11 promoters constructed, the clone 11 promoter (clone 11 + TATA-box) showed a 5-fold enhancement 6 h after the 10 Gy X-ray irradiation in HeLa cells. A mutant designated the clone 11-9-37 promoter generated through two steps of epPCR showed a sensitivity 4.8 times higher than the clone 11 pr...
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PMID: 18161064
PDF is available here.
PDF is available here.
Abstract
An 8-year-old African-American boy had a clinical history consistent with mild beta-thalassemia intermedia with moderate anemia, microcytosis, reticulocytosis, and splenomegaly. He was asymptomatic and did not require transfusion. At age 4 years, hemoglobin (Hb) electrophoresis showed Hb A = 37.8%,...
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PMID: 16732578
PDF is available here.
PDF is available here.
Abstract
We recently identified a novel human virus classifiable into a third group in the genus Anellovirus, tentatively designated torque teno midi virus (TTMDV), with a circular DNA genome of 3.2 kb and genomic organization resembling those of torque teno virus (TTV) (3.8 to 3.9 kb) and torque teno mini v...
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PMID: 18094127
PDF is available here.
PDF is available here.
DNA Sequence (19)1 2008
Abstract
We have cloned the swine eNOS promoter and analyzed its function in newborn swine pulmonary artery endothelial cells (PAECs). Analysis of the 2.1 kb 5' flanking region revealed that the swine eNOS promoter is, like its counterparts in human and other species, a TATA-less promoter. The transcription...
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PMID: 17852356
PDF is available here.
PDF is available here.
Journal of Virology (82)4 2008
Abstract
We found that the noncanonical TATA sequence is required for the accumulation of late viral transcripts. The GC boxes that surround the middle TATA element did not affect the kinetics or the start site of UL44 late transcription. Replacement of the distal TATA element with a noncanonical TATA sequen...
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PMID: 18057245
PDF is available here.
PDF is available here.
Abstract
Increased TATA-binding activity of proteins in nuclear extracts from murine hepatocarcinoma HA-1 and murine Lewis lung adenocarcinoma was demonstrated. The dependence of the amount of formed complexes on protein concentration, displacement of labeled 32P-TATA-containing oligonucleotide by its unlabe...
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PMID: 19024013
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Abstract
Genes were divided into four groups according to their core promoter type and their characteristics analyzed statistically. Surprisingly we found that small variations in the TATA box are linked to large differences in gene length. Genes containing canonical TATA are generally short whereas long gen...
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PMID: 18298820
PDF is available here.
PDF is available here.
Abstract
Genotype distributions for 1102 subjects with (TA)6 or (TA)7 alleles were as follows: 54.10%, 26.33% and 18.94% for the (TA)7/(TA)7, (TA)6/(TA)7 and (TA)6/(TA)6, respectively. Sequencing of seven samples that could not be identified as one of these alleles identified four subjects with the (TA)5/(TA...
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PMID: 18324905
PDF is available here.
PDF is available here.
BMC Genomics (9 Suppl 2)suppl 2 2008
Abstract
We found a consistently high correspondence between C+G content, CpG-island presence and an average expression level increasing the median level for all genes in bidirectional promoters. These CpG-rich promoters showed discrete initiation patterns rather than broad regions of transcription initiatio...
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PMID: 18831794
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Human and mouse switch-like genes share common transcriptional regulatory mechanisms for bimodality.
Abstract
Fourteen percent of the human genes on the HGU133A array (1847 out of 13076) were identified as bimodal or switch-like. More than 40% were found to have bimodal mouse orthologs. KEGG pathways enriched for bimodal genes included ECM-receptor interaction, focal adhesion, and tight junction, showing st...
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PMID: 19105848
PDF is available here.
PDF is available here.
Journal of General Virology (89)Pt 1 2008
Abstract
We report here the complete genome sequence of two new BPV types isolated from separate epithelial squamous papilloma lesions on cattle teats. The genomes are 7,303 and 7,399 bp in length, respectively, and both have genetic organization and consensus motifs typical of papillomaviruses. A neighbour-...
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PMID: 18089739
PDF is available here.
PDF is available here.
Journal of Virology (82)2 2008
Abstract
We determined the role of the cis-acting element in viral replication by comparing recombinant viruses with the cis-acting element replaced with other sequences. Recombinant virus with the simian CMV counterpart replicated efficiently in human foreskin fibroblasts, as well as wild-type virus. In con...
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PMID: 17989180
PDF is available here.
PDF is available here.
Abstract
Yeast recombinant plasmid containing FRT-sequence flanked by hybrid GAL-CYC promoter and NPTII gene was developed. GAL-CYC promoter contains four UAS sequences and two closely associated TATA-boxes in CYC part. This construct provides galactose-inducible synthesis of neomycinphosphotransferase from...
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PMID: 19140324
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1779)6-7 2008
Abstract
The juvenile hormone binding protein (JHBP) plays a key role in the protection and transport of the hormone to target tissues. In this report the sequence of the jhbp promoter comprising about 2000 bp is characterized. Using a minimized false positive algorithm, six putative regulatory elements, Hun...
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PMID: 18515113
PDF is available here.
PDF is available here.
Archives of Virology (153)1 2008
Abstract
The major capsid protein (mcp) gene of Spodoptera exigua ascovirus 5a (SeAV-5a) was confirmed by aphidicolin viral DNA replication inhibition analysis to be a late gene. The 5' and 3' ends of mcp gene transcripts have been mapped. Primer extension analyses indicated that transcription of the mcp gen...
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PMID: 17978884
PDF is available here.
PDF is available here.
Muscle & Nerve (36)5 2007
Abstract
We report a patient with autosomal-dominant amyotrophic lateral sclerosis (ALS) and a sequence variation in the SOD1 promoter region, located in the conserved TATA box motif (TATAAA-->TGTAAA). Functional promoter studies of this variant in an in vitro system showed moderate reduction in transcriptio...
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PMID: 17636481
PDF is available here.
PDF is available here.
Mammalian Genome (18)11 2007
Abstract
We analyzed TAF1/DYT3, a complex transcript system that is composed of at least 43 exons. Thirty-eight exons code for TATA box binding protein associated factor I (TAF1). Five downstream exons (d1-d5) of yet unknown function can either form transcripts with TAF1 exons or be transcribed independently...
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PMID: 17952504
PDF is available here.
PDF is available here.
Plant Molecular Biology (65)5 2007
Abstract
We showed that an SBP2-GFP fusion protein under the control of the GmSBP2 promoter accumulates in the vascular tissues of vegetative organs, which is consistent with the proposed involvement of SBP in sucrose transport-dependent physiological processes. Through gain-of-function experiments we confir...
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PMID: 17710554
PDF is available here.
PDF is available here.
Abstract
We genotyped five functional polymorphisms including -3279T>G and -3156G>A in the enhancer region, (TA)6>7 in the TATA box, and 211G>A (G71R), 686C>A (P229Q) in the exon1 region of UGT1A1 in three groups of healthy Chinese ethnic populations, consisting of 264 subjects of She origin, 539 of Han orig...
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PMID: 17060921
PDF is available here.
PDF is available here.
Journal of Molecular Biology (372)3 2007
Abstract
We have used quantitative solution fluorescence resonance energy transfer (FRET) and gel-based FRET (gelFRET) to determine the effect of TFIIA on the conformation of the DNA in TBP/TATA complexes and on the kinetic stability of these complexes. Our results indicate that human TFIIA decreases the ang...
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PMID: 17681538
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (282)34 2007
Abstract
We report that a functional INR provides resistance to NC2 (Dr1/DRAP1), a general repressor of TATA promoters. INR-mediated resistance to NC2 is established during transcription initiation complex assembly and requires TBP-associated factors (TAFs) and TAF- and INR-dependent cofactor activity. Remar...
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PMID: 17584739
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (282)33 2007
Abstract
We obtained a comprehensive view of this transcriptional program. As expected, we identified both rapid and delayed gene inductions. Surprisingly, however, a large fraction of genes induced with delayed kinetics did not require protein synthesis and therefore represented delayed primary rather than...
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PMID: 17575275
PDF is available here.
PDF is available here.
Abstract
Abstract
The molecular defects of beta- thalassemia intermedia in Guangdong Province were highly heterogeneous and its spectrum was different from the reports from other provinces of China....
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PMID: 17706040
PDF is available here.
PDF is available here.
Abstract
We looked for the existence of other promoters that may direct the expression of aromatase in adult rat germ cells. Besides the promoter II, we have shown the presence of transcripts derived from the brain promoter PI.f in spermatogonia-preleptotene spermatocytes (G-PL), pachytene spermatocytes (PS)...
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PMID: 17693615
PDF is available here.
PDF is available here.
Abstract
Antiviral Research (75)2 2007
Abstract
We performed a genome-wide fold recognition search to identify viral proteins potentially recognizing the TATT-box. By applying profile-profile comparisons and homology-based protein structure prediction we identified a protein of unknown function from Gammaherpesvirinae (BcRF1 of EBV) and their Bet...
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PMID: 17400302
PDF is available here.
PDF is available here.
Abstract
We constructed and analyzed reporters in which the UAS-TATA distance varied. Our results show that UASs lose the ability to activate normal transcription as the UAS-TATA distance increases. Surprisingly, transcription does initiate, but proximally to the UAS, regardless of its location. To identify...
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PMID: 17526727
PDF is available here.
PDF is available here.