PMID-sentid Pub_year Sent_text comp_official_name comp_offsetprotein_name organism prot_offset 21058683-3 2010 As an example, reverse transcription of the HIV genome is primed by a human lysine-specific tRNA (tRNA(Lys3)) that is packaged (into the virion) by the HIV Gag protein with lysyl-tRNA synthetase (LysRS). Lysine 76-82 mitochondrially encoded tRNA glycine Homo sapiens 98-108 21058683-3 2010 As an example, reverse transcription of the HIV genome is primed by a human lysine-specific tRNA (tRNA(Lys3)) that is packaged (into the virion) by the HIV Gag protein with lysyl-tRNA synthetase (LysRS). Lysine 76-82 lysyl-tRNA synthetase 1 Homo sapiens 173-194 21058683-3 2010 As an example, reverse transcription of the HIV genome is primed by a human lysine-specific tRNA (tRNA(Lys3)) that is packaged (into the virion) by the HIV Gag protein with lysyl-tRNA synthetase (LysRS). Lysine 76-82 lysyl-tRNA synthetase 1 Homo sapiens 196-201 21058683-5 2010 Here, ab initio computational methods, together with our recent high-resolution 3-D structure of human LysRS, produced an energy-minimized model where Gag, tRNA(Lys), and LysRS form a ternary complex. Glycosaminoglycans 151-154 lysyl-tRNA synthetase 1 Homo sapiens 103-108 21058683-5 2010 Here, ab initio computational methods, together with our recent high-resolution 3-D structure of human LysRS, produced an energy-minimized model where Gag, tRNA(Lys), and LysRS form a ternary complex. Glycosaminoglycans 151-154 lysyl-tRNA synthetase 1 Homo sapiens 171-176 21058683-6 2010 Interestingly, the model requires normally homodimeric LysRS to dissociate into a monomer that bridges between Gag and tRNA(Lys3). Glycosaminoglycans 111-114 lysyl-tRNA synthetase 1 Homo sapiens 55-60 19701194-7 2009 The miR-26 family of miRNAs targets IL-6, and the addition of terminal uridines to the miR-26 3" end abrogates IL-6 repression. Uridine 71-79 interleukin 6 Homo sapiens 36-40 19494110-7 2009 In mNect.hCNT3-expressing cells (but not under negative control conditions) the rate of acidification increased in media containing 0.5 mm uridine, providing the first direct evidence for H(+)-coupled uridine transport. Uridine 139-146 solute carrier family 28 member 3 Homo sapiens 9-14 19701194-7 2009 The miR-26 family of miRNAs targets IL-6, and the addition of terminal uridines to the miR-26 3" end abrogates IL-6 repression. Uridine 71-79 interleukin 6 Homo sapiens 111-115 19701194-8 2009 Whereas 78% of miR-26a sequences in control cells contained 1-3 uridines on their 3" ends, less than 0.1% did so in Zcchc11-knockdown cells. Uridine 64-72 microRNA 26a-1 Homo sapiens 15-22 19435930-1 2009 The mRNA-destabilizing protein tristetraprolin (TTP) negatively regulates adenine- and uridine-rich element (ARE)-containing mRNAs. Uridine 87-94 ZFP36 ring finger protein Homo sapiens 48-51 19520857-0 2009 B cell lymphoma (Bcl)-2 protein is the major determinant in bcl-2 adenine-uridine-rich element turnover overcoming HuR activity. Uridine 74-81 BCL2 apoptosis regulator Homo sapiens 0-23 19520857-0 2009 B cell lymphoma (Bcl)-2 protein is the major determinant in bcl-2 adenine-uridine-rich element turnover overcoming HuR activity. Uridine 74-81 BCL2 apoptosis regulator Homo sapiens 60-65 19520857-0 2009 B cell lymphoma (Bcl)-2 protein is the major determinant in bcl-2 adenine-uridine-rich element turnover overcoming HuR activity. Uridine 74-81 ELAV like RNA binding protein 1 Homo sapiens 115-118 19435930-1 2009 The mRNA-destabilizing protein tristetraprolin (TTP) negatively regulates adenine- and uridine-rich element (ARE)-containing mRNAs. Uridine 87-94 ZFP36 ring finger protein Homo sapiens 31-46 19494110-7 2009 In mNect.hCNT3-expressing cells (but not under negative control conditions) the rate of acidification increased in media containing 0.5 mm uridine, providing the first direct evidence for H(+)-coupled uridine transport. Uridine 201-208 solute carrier family 28 member 3 Homo sapiens 9-14 19532987-4 2009 We have investigated the mechanism of human uridine-cytidine kinase 2 (UCK2, EC 2.7.1.48), which catalyzes the transfer of a phosphate group from ATP to the ribose 5"-hydroxyl of cytidine and uridine. Uridine 44-51 uridine-cytidine kinase 2 Homo sapiens 71-75 19585516-2 2009 APOBEC3G (A3G) is an intracellular anti-viral factor that deaminates cytidine to uridine. Uridine 81-88 apolipoprotein B mRNA editing enzyme catalytic subunit 3G Homo sapiens 0-8 19585516-2 2009 APOBEC3G (A3G) is an intracellular anti-viral factor that deaminates cytidine to uridine. Uridine 81-88 apolipoprotein B mRNA editing enzyme catalytic subunit 3G Homo sapiens 10-13 19593383-4 2009 Here we show that in Caenorhabditis elegans, ELPC-1 and ELPC-3, components of the Elongator complex, are required for the formation of the 5-carbamoylmethyl and 5-methylcarboxymethyl side chains of wobble uridines in tRNA. Uridine 205-213 Elongator complex protein 1 Caenorhabditis elegans 45-51 19593383-4 2009 Here we show that in Caenorhabditis elegans, ELPC-1 and ELPC-3, components of the Elongator complex, are required for the formation of the 5-carbamoylmethyl and 5-methylcarboxymethyl side chains of wobble uridines in tRNA. Uridine 205-213 Elongator complex protein 3 Caenorhabditis elegans 56-62 19481523-1 2009 H/ACA RNAs form ribonucleoprotein complex (RNP) with proteins Cbf5, Nop10, L7Ae, and Gar1 and guide site-specific conversion of uridine into pseudouridine in cellular RNAs. Uridine 128-135 dyskerin pseudouridine synthase 1 Homo sapiens 62-66 19389408-3 2009 A3G deaminates cytidines to uridines in single-strand DNA and inhibits the replication of human immunodeficiency virus-1, other retroviruses, and retrotransposons. Uridine 28-36 apolipoprotein B mRNA editing enzyme catalytic subunit 3G Homo sapiens 0-3 19460866-5 2009 Siwi-bound piRNAs have a strong bias for uridine at their 5" end and BmAgo3-bound piRNAs are enriched for adenine at position 10. Uridine 41-48 piwi-like protein Siwi Bombyx mori 0-4 19460866-5 2009 Siwi-bound piRNAs have a strong bias for uridine at their 5" end and BmAgo3-bound piRNAs are enriched for adenine at position 10. Uridine 41-48 piwi-like protein Ago3 Bombyx mori 69-75 19481523-1 2009 H/ACA RNAs form ribonucleoprotein complex (RNP) with proteins Cbf5, Nop10, L7Ae, and Gar1 and guide site-specific conversion of uridine into pseudouridine in cellular RNAs. Uridine 128-135 NOP10 ribonucleoprotein Homo sapiens 68-73 19481523-1 2009 H/ACA RNAs form ribonucleoprotein complex (RNP) with proteins Cbf5, Nop10, L7Ae, and Gar1 and guide site-specific conversion of uridine into pseudouridine in cellular RNAs. Uridine 128-135 GAR1 ribonucleoprotein Homo sapiens 85-89 19404339-5 2009 The 3"-UTR ADAMTS1 mRNA contains multiple adenine and uridine-rich elements, suggesting that the 3"-UTR may regulate gene stability. Uridine 54-61 ADAM metallopeptidase with thrombospondin type 1 motif 1 Homo sapiens 11-18 19038776-3 2009 In the absence of Vif, APOBEC3G/F are encapsidated by budding virus particles leading to excessive cytidine (C) to uridine (U) editing of negative sense reverse transcripts in newly infected cells. Uridine 115-122 apolipoprotein B mRNA editing enzyme catalytic subunit 3G Homo sapiens 23-31 20049701-3 2009 In vitro, COX-deficient human cells require additional glucose, pyruvate and uridine for normal growth and are specifically sensitive to oxidative stress. Uridine 77-84 cytochrome c oxidase subunit 8A Homo sapiens 10-13 19135251-9 2009 Uridine uptake was inhibited by ENT1 and ENT2 substrates, and ddI uptake was also inhibited by substrates or inhibitors at concentrations that inhibit ENT2. Uridine 0-7 solute carrier family 29 member 1 Rattus norvegicus 32-36 19084567-1 2009 APOBEC3G is an innate intracellular anti-viral factor which deaminates retroviral cytidine to uridine. Uridine 94-101 apolipoprotein B mRNA editing enzyme catalytic subunit 3G Homo sapiens 0-8 19266078-1 2009 The human cytidine deaminase APOBEC3G (A3G) is a potent inhibitor of retroviruses and transposable elements and is able to deaminate cytidines to uridines in single-stranded DNA replication intermediates. Uridine 146-154 apolipoprotein B mRNA editing enzyme catalytic subunit 3G Homo sapiens 29-37 19266078-1 2009 The human cytidine deaminase APOBEC3G (A3G) is a potent inhibitor of retroviruses and transposable elements and is able to deaminate cytidines to uridines in single-stranded DNA replication intermediates. Uridine 146-154 apolipoprotein B mRNA editing enzyme catalytic subunit 3G Homo sapiens 39-42 19202054-2 2009 The DNA deamination model assumes that AID deaminates cytidine (C) on DNA and generates uridine (U), resulting in DNA cleavage after removal of U by uracil DNA glycosylase (UNG). Uridine 88-95 activation induced cytidine deaminase Homo sapiens 39-42 19202054-2 2009 The DNA deamination model assumes that AID deaminates cytidine (C) on DNA and generates uridine (U), resulting in DNA cleavage after removal of U by uracil DNA glycosylase (UNG). Uridine 88-95 uracil DNA glycosylase Homo sapiens 149-171 19202054-2 2009 The DNA deamination model assumes that AID deaminates cytidine (C) on DNA and generates uridine (U), resulting in DNA cleavage after removal of U by uracil DNA glycosylase (UNG). Uridine 88-95 uracil DNA glycosylase Homo sapiens 173-176 19020091-3 2008 CoQ oxidation by AOX reduces the dependence of rho degrees cells on pyruvate and uridine. Uridine 81-88 acyl-CoA oxidase 1 Homo sapiens 17-20 18606862-5 2008 (Uridine probably acts by generating both CTP, which can be limiting in phosphatide synthesis, and UTP, which activates P2Y receptors coupled to neurite outgrowth and protein synthesis. Uridine 1-8 solute carrier family 25 member 1 Homo sapiens 42-45 18664566-1 2008 The wobble uridine in yeast cytosolic tRNA(Lys2)(UUU) and tRNA(Glu3)(UUC) undergoes a thio-modification at the second position (s(2) modification) and a methoxycarbonylmethyl modification at the fifth position (mcm(5) modification). Uridine 11-18 L-aminoadipate-semialdehyde dehydrogenase Saccharomyces cerevisiae S288C 38-47 19198146-2 2008 Crucial molecular mechanism includes a lack of taurine modification at the wobble uridine of the mutant tRNA(Leu(UUR)), causing UUG condon-specific translational defect and mitochondrial protein synthesis failure. Uridine 82-89 mitochondrially encoded tRNA glycine Homo sapiens 104-117 18423905-3 2008 Brain phosphatidylcholine (PC) synthesis utilizes both the uridine formed from the metabolism of exogenous CDP-choline and UMP, and the choline formed from that of CDP-choline. Uridine 59-66 cut-like homeobox 1 Rattus norvegicus 107-110 18648068-1 2008 Pseudouridine synthase 1 (Pus1p) is an enzyme that converts uridine to Pseudouridine (Psi) in tRNA and other RNAs in eukaryotes. Uridine 6-13 pseudouridine synthase 1 Homo sapiens 26-31 18630897-3 2008 Among the synthesized uridine derivatives, we identified the first potent and selective inhibitors of human NTPDase2. Uridine 22-29 ectonucleoside triphosphate diphosphohydrolase 2 Homo sapiens 108-116 18755836-8 2008 Pseudouridine is the preferred substrate as revealed by the inability of YbeA to methylate uridine at position 1915. Uridine 6-13 hypothetical protein Escherichia coli 73-77 18599582-4 2008 Suppression of variegation in the first line, TAG-FN, was caused by disruption of the nuclear gene (SUPPRESSOR OF VARIEGATION1 [SVR1]) for a chloroplast-localized homolog of pseudouridine (Psi) synthase, which isomerizes uridine to Psi in noncoding RNAs. Uridine 180-187 pseudouridine synthase family protein Arabidopsis thaliana 100-126 18621711-1 2008 In vertebrates, assembly of spliceosomal uridine-rich small nuclear ribonucleoproteins (UsnRNPs) is mediated by the SMN complex, a macromolecular entity composed of the proteins SMN and Gemins 2-8. Uridine 41-48 Gemin 2 Drosophila melanogaster 186-196 18505733-3 2008 We showed previously that two adenosine/uridine-rich elements (ARE) in this splice-deleted region of CD3zeta transcript are critical for the mRNA stability and protein expression of CD3zeta. Uridine 40-47 CD247 molecule Homo sapiens 101-108 18505733-3 2008 We showed previously that two adenosine/uridine-rich elements (ARE) in this splice-deleted region of CD3zeta transcript are critical for the mRNA stability and protein expression of CD3zeta. Uridine 40-47 CD247 molecule Homo sapiens 182-189 18599582-4 2008 Suppression of variegation in the first line, TAG-FN, was caused by disruption of the nuclear gene (SUPPRESSOR OF VARIEGATION1 [SVR1]) for a chloroplast-localized homolog of pseudouridine (Psi) synthase, which isomerizes uridine to Psi in noncoding RNAs. Uridine 180-187 pseudouridine synthase family protein Arabidopsis thaliana 128-132 18599582-10 2008 In planta mutagenesis revealed that SVR1 not only played a role in uridine isomerization but that its physical presence was necessary for proper chloroplast rRNA processing. Uridine 67-74 pseudouridine synthase family protein Arabidopsis thaliana 36-40 18500819-7 2008 Interestingly, this characteristic beta-loop structure is conserved among a number of RRMs, including the U2AF65 RRM2 and the Sex-lethal RRM1 and RRM2, which also bind to uridine-rich RNAs. Uridine 171-178 ribonucleotide reductase M1 Mus musculus 137-141 18500819-7 2008 Interestingly, this characteristic beta-loop structure is conserved among a number of RRMs, including the U2AF65 RRM2 and the Sex-lethal RRM1 and RRM2, which also bind to uridine-rich RNAs. Uridine 171-178 ribonucleotide reductase M2 Mus musculus 146-150 18500819-3 2008 The second RRM (RRM2) is necessary and sufficient for tight, sequence-specific binding to the uridine-rich sequences buried around the 5" splice sites. Uridine 94-101 ribonucleotide reductase M2 Mus musculus 11-14 18500819-3 2008 The second RRM (RRM2) is necessary and sufficient for tight, sequence-specific binding to the uridine-rich sequences buried around the 5" splice sites. Uridine 94-101 ribonucleotide reductase M2 Mus musculus 16-20 18600533-5 2008 Uridine rescue in mice allowed 1.5-fold increase in 5FU dose, leading to 2-fold increase in the antitumor effect and thymidylate synthase inhibition in resistant Colon-26 tumors. Uridine 0-7 thymidylate synthase Mus musculus 117-137 18500819-7 2008 Interestingly, this characteristic beta-loop structure is conserved among a number of RRMs, including the U2AF65 RRM2 and the Sex-lethal RRM1 and RRM2, which also bind to uridine-rich RNAs. Uridine 171-178 ribonucleotide reductase M2 Mus musculus 113-117 18313046-11 2008 Intravenous 8-cyclopenthyl-1,3-dipropylxanthine (DPCPX) (5 mg/kg), a selective adenosine A(1) receptor antagonist, greatly attenuated the cardiovascular responses to uridine and cytidine. Uridine 166-173 adenosine A1 receptor Rattus norvegicus 79-102 18329095-6 2008 These results are consistent with the reported uptake characteristics of uridine and adenosine by ENT1 and ENT2. Uridine 73-80 solute carrier family 29 member 1 Rattus norvegicus 98-102 18313046-19 2008 The data also implicates that the mainly adenosine A(1) receptor activation is involved in the uridine-induced cardiovascular effects, while both adenosine A(1) and A(2A) receptor activations mediate the cytidine"s effects. Uridine 95-102 adenosine A1 receptor Rattus norvegicus 41-64 18549497-4 2008 The PY tract is a uridine-rich region at the 3" end of introns that acts as a binding site for U2AF65, a key factor in splicing machinery recruitment. Uridine 18-25 U2 small nuclear RNA auxiliary factor 2 Homo sapiens 95-101 18292547-7 2008 In contrast, 2"-O-methyl groups at adenosine and uridine residues reduced both IFN-alpha secretion and gene-silencing activity. Uridine 49-56 interferon alpha 1 Homo sapiens 79-88 18598372-1 2008 The AID/APOBECs, a group of cytidine deaminases, represent a somewhat unusual protein family that can insert mutations in DNA and RNA as a result of their ability to deaminate cytidine to uridine. Uridine 188-195 activation induced cytidine deaminase Homo sapiens 4-7 18342361-5 2008 We found that AGO2 and AGO4 preferentially recruit small RNAs with a 5" terminal adenosine, whereas AGO1 harbors microRNAs (miRNAs) that favor a 5" terminal uridine. Uridine 157-164 Argonaute family protein Arabidopsis thaliana 14-18 18342361-5 2008 We found that AGO2 and AGO4 preferentially recruit small RNAs with a 5" terminal adenosine, whereas AGO1 harbors microRNAs (miRNAs) that favor a 5" terminal uridine. Uridine 157-164 Stabilizer of iron transporter SufD / Polynucleotidyl transferase Arabidopsis thaliana 100-104 18199742-6 2008 Access of this membrane-impermeant probe to Cys-561, as determined by inhibition of hCNT3 transport activity, required H(+), but not Na(+), and was blocked by extracellular uridine. Uridine 173-180 solute carrier family 28 member 3 Homo sapiens 84-89 18201561-1 2008 T-cell-restricted intracellular antigen-1 (TIA-1) regulates alternative pre-mRNA splicing in the nucleus, and mRNA translation in the cytoplasm, by recognizing uridine-rich sequences of RNAs. Uridine 160-167 TIA1 cytotoxic granule associated RNA binding protein Homo sapiens 0-41 18201561-1 2008 T-cell-restricted intracellular antigen-1 (TIA-1) regulates alternative pre-mRNA splicing in the nucleus, and mRNA translation in the cytoplasm, by recognizing uridine-rich sequences of RNAs. Uridine 160-167 TIA1 cytotoxic granule associated RNA binding protein Homo sapiens 43-48 18344610-9 2008 mRNAs of nucleoside transporter (NT), ENT1, ENT2, CNT, and CNT3 were expressed in neutrophils; and their inhibitors, inosine, uridine, and s-(4-nitrobenzyl)-6-thioinosine, reduced the [Ca(2+)](i) rise induced by beta-NAD(+) and fMLP. Uridine 126-133 solute carrier family 28 member 3 Homo sapiens 59-63 18082610-3 2007 Trm9 methylates the uridine wobble base of tRNAARG(UCU) and tRNAGLU(UUC). Uridine 20-27 tRNA (carboxymethyluridine(34)-5-O)-methyltransferase Saccharomyces cerevisiae S288C 0-4 18155131-6 2007 These effects of Dnd1 are mediated through uridine-rich regions present in the miRNA-targeted mRNAs. Uridine 43-50 DND microRNA-mediated repression inhibitor 1 Homo sapiens 17-21 18028944-1 2007 The nuclear import of assembled spliceosomal subunits, the uridine-rich small nuclear ribonucleoprotein particles (U snRNPs), is mediated by a nuclear import receptor adaptor couple of importin beta (Imp beta) and snurportin1 (SPN1). Uridine 59-66 snurportin 1 Homo sapiens 214-225 18028944-1 2007 The nuclear import of assembled spliceosomal subunits, the uridine-rich small nuclear ribonucleoprotein particles (U snRNPs), is mediated by a nuclear import receptor adaptor couple of importin beta (Imp beta) and snurportin1 (SPN1). Uridine 59-66 snurportin 1 Homo sapiens 227-231 17890166-6 2007 Furthermore, the substrate binding pocket of uridine-cytidine kinase (or uridine kinase) has localized sequence similarity with ZAP3, suggesting uridine or cytidine as possible ZAP3 substrates. Uridine 45-52 YLP motif containing 1 Homo sapiens 128-132 18059286-4 2007 Our structural and complementary fluorescence analyses also indicate that precise placement of the target uridine at the active site requires a conformation of the guide-substrate RNA duplex that is brought about by the previously identified concurrent interaction of the guide RNA with L7Ae and a composite Cbf5-Nop10 surface, and further identify a residue that is critical in this process. Uridine 106-113 dyskerin pseudouridine synthase 1 Homo sapiens 308-312 18059286-4 2007 Our structural and complementary fluorescence analyses also indicate that precise placement of the target uridine at the active site requires a conformation of the guide-substrate RNA duplex that is brought about by the previously identified concurrent interaction of the guide RNA with L7Ae and a composite Cbf5-Nop10 surface, and further identify a residue that is critical in this process. Uridine 106-113 NOP10 ribonucleoprotein Homo sapiens 313-318 17704058-11 2007 Glu-322, the residue having the greatest influence on hCNT1 transport function, exhibited uridine-protected inhibition by p-chloromercuriphenyl sulfonate and 2-aminoethyl methanethiosulfonate when converted to cysteine. Uridine 90-97 solute carrier family 28 member 1 Homo sapiens 54-59 17890166-6 2007 Furthermore, the substrate binding pocket of uridine-cytidine kinase (or uridine kinase) has localized sequence similarity with ZAP3, suggesting uridine or cytidine as possible ZAP3 substrates. Uridine 45-52 YLP motif containing 1 Homo sapiens 177-181 17630326-0 2007 Influence of C-5 halogenation of uridines on hairpin versus duplex RNA folding. Uridine 33-41 complement C5 Homo sapiens 13-16 17696452-10 2007 Apparent Km and Vmax values were 17 microM and 7.2 nmol x min(-1) x cm(-2), and transport selectivity was adenosine = inosine = uridine > guanosine = cytidine > thymidine. Uridine 128-135 CD59 molecule (CD59 blood group) Homo sapiens 58-64 17700367-6 2007 Expression of these variants in U-251 cells revealed that all except E385K can uptake various substrates of hCNT2: inosine, ribavirin and uridine. Uridine 138-145 solute carrier family 28 member 2 Homo sapiens 108-113 17570319-9 2007 Uridine appeared to affect the tumour necrosis factor (TNF) levels, although this could not be statistically confirmed due to large variations within the Sephadex control group. Uridine 0-7 tumor necrosis factor Rattus norvegicus 31-53 17570319-9 2007 Uridine appeared to affect the tumour necrosis factor (TNF) levels, although this could not be statistically confirmed due to large variations within the Sephadex control group. Uridine 0-7 tumor necrosis factor Rattus norvegicus 55-58 17466948-7 2007 Here we found that PTB (Polypyrimidine Tract-Binding Protein) is a novel member of the ribonucleoprotein complex that interacts with the beta-F1-ATPase mRNA through an adenosine/uridine (AU)-rich element located to the beta-F1-ATPase 3"-untranslated region (beta-3"-UTR). Uridine 178-185 polypyrimidine tract binding protein 1 Homo sapiens 19-22 17592039-6 2007 Deletion of the TUC1 gene together with a deletion of the ELP3 gene, which results in the lack of the mcm(5) side chain, removes all modifications from the wobble uridine derivatives of the cytoplasmic tRNAs specific for Gln, Lys, and Glu, and is lethal to the cell. Uridine 163-170 Ncs6p Saccharomyces cerevisiae S288C 16-20 17592039-6 2007 Deletion of the TUC1 gene together with a deletion of the ELP3 gene, which results in the lack of the mcm(5) side chain, removes all modifications from the wobble uridine derivatives of the cytoplasmic tRNAs specific for Gln, Lys, and Glu, and is lethal to the cell. Uridine 163-170 Elongator subunit ELP3 Saccharomyces cerevisiae S288C 58-62 17548472-3 2007 Here we show that the RNA-binding protein HuR stabilizes the beta-actin mRNA by associating with a uridine-rich element within its 3" untranslated region. Uridine 99-106 ELAV like RNA binding protein 1 Homo sapiens 42-45 17548472-3 2007 Here we show that the RNA-binding protein HuR stabilizes the beta-actin mRNA by associating with a uridine-rich element within its 3" untranslated region. Uridine 99-106 POTE ankyrin domain family member F Homo sapiens 61-71 17466948-7 2007 Here we found that PTB (Polypyrimidine Tract-Binding Protein) is a novel member of the ribonucleoprotein complex that interacts with the beta-F1-ATPase mRNA through an adenosine/uridine (AU)-rich element located to the beta-F1-ATPase 3"-untranslated region (beta-3"-UTR). Uridine 178-185 polypyrimidine tract binding protein 1 Homo sapiens 24-60 17322634-0 2007 Plasma levels of uridine correlate with blood pressure and indicators of myogenic purine degradation and insulin resistance in hypertensive patients. Uridine 17-24 insulin Homo sapiens 105-112 17473171-1 2007 It has been proposed that defects in the assembly of spliceosomal uridine-rich small nuclear ribonucleoprotein (U snRNP) complexes could account for the death of motor neurons in spinal muscular atrophy (SMA). Uridine 66-73 LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated Homo sapiens 114-119 17283054-1 2007 Defects in the yeast cysteine desulfurase Nfs1 cause a severe impairment in the 2-thio modification of uridine of mitochondrial tRNAs (mt-tRNAs) and cytosolic tRNAs (cy-tRNAs). Uridine 103-110 cysteine desulfurase Saccharomyces cerevisiae S288C 42-46 17565373-5 2007 METHODOLOGY/PRINCIPAL FINDINGS: Here we have used a computational approach that combines a series of biological constraints to identify uridine-rich sequence motifs that are present within relevant biological contexts and thus are potential targets of the Drosophila master sex-switch protein Sex-lethal (SXL). Uridine 136-143 Sex lethal Drosophila melanogaster 293-303 17565373-5 2007 METHODOLOGY/PRINCIPAL FINDINGS: Here we have used a computational approach that combines a series of biological constraints to identify uridine-rich sequence motifs that are present within relevant biological contexts and thus are potential targets of the Drosophila master sex-switch protein Sex-lethal (SXL). Uridine 136-143 Sex lethal Drosophila melanogaster 305-308 17608024-1 2007 Genetic polymorphisms of uridine 5"-diphospho-glucuronosyl-transferase (UGT)1A1, a crucial drug-metabolizing enzyme of the anticancer drug irinotecan, are essential determinants of individual variation in susceptibility to irinotecan-related toxicity. Uridine 25-32 UDP glucuronosyltransferase family 1 member A1 Homo sapiens 72-79 17322634-5 2007 Fasting plasma insulin levels and homeostasis model assessment of IR correlated with plasma uridine levels in the HT patients. Uridine 92-99 insulin Homo sapiens 15-22 17253988-5 2007 T-DNA insertional mutant plants for AtENT3 resemble the fur1 mutant phenotype: i.e. they grow on fluorouridine, and seedlings as well as leaf discs exhibit a markedly reduced uptake capacity for uridine and cytidine, but a less pronounced reduced uptake for adenosine and guanosine. Uridine 103-110 Major facilitator superfamily protein Arabidopsis thaliana 36-42 17279631-5 2007 hCNT1 mutation S353T produced a profound decrease in cytidine transport efficiency (Vmax/Km ratio) and, in combination with L354V (S353T/L354V), resulted in a novel uridine-preferring transport phenotype. Uridine 165-172 solute carrier family 28 member 1 Homo sapiens 0-5 17184749-1 2007 The biosynthesis of brain membrane phosphatides, e.g., phosphatidylcholine (PtdCho), may utilize three circulating compounds: choline, uridine (a precursor for UTP, CTP, and CDP-choline), and a PUFA (e.g., docosahexaenoic acid); moreover, oral administration of the uridine source uridine-5"-monophosphate (UMP) can significantly increase levels of the phosphatides throughout the rodent brain. Uridine 135-142 cut-like homeobox 1 Rattus norvegicus 174-177 17279631-7 2007 Both hCNT1 TM 8 residues exhibited uridine-protectable inhibition by p-chloromercuribenzene sulfonate when converted to Cys, suggesting that they occupy positions within or closely adjacent to a common cation/nucleoside translocation pore. Uridine 35-42 solute carrier family 28 member 1 Homo sapiens 5-10 17279631-7 2007 Both hCNT1 TM 8 residues exhibited uridine-protectable inhibition by p-chloromercuribenzene sulfonate when converted to Cys, suggesting that they occupy positions within or closely adjacent to a common cation/nucleoside translocation pore. Uridine 35-42 tetraspanin 16 Homo sapiens 11-15 17288565-7 2007 Biochemical analyses using RNA pull-down, RNA immunoprecipitation and gel shift experiments demonstrated that adenine- and uridine-rich element-binding proteins, HuR and tristetraprolin itself, were associated with tristetraprolin adenine- and uridine-rich elements. Uridine 123-130 ELAV like RNA binding protein 1 Homo sapiens 162-165 17121826-9 2007 Interestingly, mutant E206Q, which possesses the equivalent residue in ENT1, gained uridine transport activity. Uridine 84-91 solute carrier family 29 member 1 (Augustine blood group) Homo sapiens 71-75 17003224-3 2007 The 3"-untranslated region (3"-UTR) of SLK mRNA contains multiple adenine and uridine-rich elements, suggesting that 3"-UTR may regulate mRNA stability. Uridine 78-85 STE20 like kinase Homo sapiens 39-42 17121826-4 2007 By constructing chimeras between human PMAT and ENT1, we showed that a chimera consisting of transmembrane domains (TM) 1-6 of PMAT and TM7-11 of hENT1 behaved like PMAT, transporting 1-methyl-4-phenylpyridinium (MPP+, an organic cation) but not uridine (a nucleoside), suggesting that TM1-6 contains critical domains responsible for substrate recognition. Uridine 246-253 solute carrier family 29 member 4 Homo sapiens 39-43 17121826-4 2007 By constructing chimeras between human PMAT and ENT1, we showed that a chimera consisting of transmembrane domains (TM) 1-6 of PMAT and TM7-11 of hENT1 behaved like PMAT, transporting 1-methyl-4-phenylpyridinium (MPP+, an organic cation) but not uridine (a nucleoside), suggesting that TM1-6 contains critical domains responsible for substrate recognition. Uridine 246-253 solute carrier family 29 member 1 (Augustine blood group) Homo sapiens 48-52 17121826-4 2007 By constructing chimeras between human PMAT and ENT1, we showed that a chimera consisting of transmembrane domains (TM) 1-6 of PMAT and TM7-11 of hENT1 behaved like PMAT, transporting 1-methyl-4-phenylpyridinium (MPP+, an organic cation) but not uridine (a nucleoside), suggesting that TM1-6 contains critical domains responsible for substrate recognition. Uridine 246-253 solute carrier family 29 member 4 Homo sapiens 127-131 17121826-4 2007 By constructing chimeras between human PMAT and ENT1, we showed that a chimera consisting of transmembrane domains (TM) 1-6 of PMAT and TM7-11 of hENT1 behaved like PMAT, transporting 1-methyl-4-phenylpyridinium (MPP+, an organic cation) but not uridine (a nucleoside), suggesting that TM1-6 contains critical domains responsible for substrate recognition. Uridine 246-253 solute carrier family 29 member 1 (Augustine blood group) Homo sapiens 146-151 17121826-4 2007 By constructing chimeras between human PMAT and ENT1, we showed that a chimera consisting of transmembrane domains (TM) 1-6 of PMAT and TM7-11 of hENT1 behaved like PMAT, transporting 1-methyl-4-phenylpyridinium (MPP+, an organic cation) but not uridine (a nucleoside), suggesting that TM1-6 contains critical domains responsible for substrate recognition. Uridine 246-253 solute carrier family 29 member 4 Homo sapiens 127-131 17288565-7 2007 Biochemical analyses using RNA pull-down, RNA immunoprecipitation and gel shift experiments demonstrated that adenine- and uridine-rich element-binding proteins, HuR and tristetraprolin itself, were associated with tristetraprolin adenine- and uridine-rich elements. Uridine 123-130 ZFP36 ring finger protein Homo sapiens 170-185 17288565-7 2007 Biochemical analyses using RNA pull-down, RNA immunoprecipitation and gel shift experiments demonstrated that adenine- and uridine-rich element-binding proteins, HuR and tristetraprolin itself, were associated with tristetraprolin adenine- and uridine-rich elements. Uridine 123-130 ZFP36 ring finger protein Homo sapiens 215-230 17288565-7 2007 Biochemical analyses using RNA pull-down, RNA immunoprecipitation and gel shift experiments demonstrated that adenine- and uridine-rich element-binding proteins, HuR and tristetraprolin itself, were associated with tristetraprolin adenine- and uridine-rich elements. Uridine 244-251 ELAV like RNA binding protein 1 Homo sapiens 162-165 17288565-7 2007 Biochemical analyses using RNA pull-down, RNA immunoprecipitation and gel shift experiments demonstrated that adenine- and uridine-rich element-binding proteins, HuR and tristetraprolin itself, were associated with tristetraprolin adenine- and uridine-rich elements. Uridine 244-251 ZFP36 ring finger protein Homo sapiens 170-185 17288565-7 2007 Biochemical analyses using RNA pull-down, RNA immunoprecipitation and gel shift experiments demonstrated that adenine- and uridine-rich element-binding proteins, HuR and tristetraprolin itself, were associated with tristetraprolin adenine- and uridine-rich elements. Uridine 244-251 ZFP36 ring finger protein Homo sapiens 215-230 17237417-1 2007 Apolipoprotein B mRNA-editing, enzyme-catalytic, polypeptide-like-3G (A3G) is an intracellular innate antiviral factor that deaminates retroviral cytidine to uridine. Uridine 158-165 apolipoprotein B mRNA editing enzyme catalytic subunit 3G Homo sapiens 0-68 17237417-1 2007 Apolipoprotein B mRNA-editing, enzyme-catalytic, polypeptide-like-3G (A3G) is an intracellular innate antiviral factor that deaminates retroviral cytidine to uridine. Uridine 158-165 apolipoprotein B mRNA editing enzyme catalytic subunit 3G Homo sapiens 70-73 17135269-2 2007 TIA-1 (T-cell intracellular antigen 1) and TIAR (TIA-1-related) proteins regulate alternative pre-mRNA splicing by promoting the use of suboptimal 5" splice sites followed by uridine-rich intronic enhancer sequences. Uridine 175-182 TIA1 cytotoxic granule associated RNA binding protein Homo sapiens 0-5 17464349-1 2007 Human cytidine deaminase (HCD) catalyzes the deamination of cytidine or deoxycytidine to uridine or deoxyuridine, respectively. Uridine 89-96 cytidine deaminase Homo sapiens 6-24 17135269-2 2007 TIA-1 (T-cell intracellular antigen 1) and TIAR (TIA-1-related) proteins regulate alternative pre-mRNA splicing by promoting the use of suboptimal 5" splice sites followed by uridine-rich intronic enhancer sequences. Uridine 175-182 TIA1 cytotoxic granule associated RNA binding protein Homo sapiens 7-37 17135269-2 2007 TIA-1 (T-cell intracellular antigen 1) and TIAR (TIA-1-related) proteins regulate alternative pre-mRNA splicing by promoting the use of suboptimal 5" splice sites followed by uridine-rich intronic enhancer sequences. Uridine 175-182 TIA1 cytotoxic granule associated RNA binding protein like 1 Homo sapiens 43-47 17135269-2 2007 TIA-1 (T-cell intracellular antigen 1) and TIAR (TIA-1-related) proteins regulate alternative pre-mRNA splicing by promoting the use of suboptimal 5" splice sites followed by uridine-rich intronic enhancer sequences. Uridine 175-182 TIA1 cytotoxic granule associated RNA binding protein Homo sapiens 49-54 17018299-1 2006 The Saccharomyces cerevisiae Elongator complex consisting of the six Elp1-Elp6 proteins has been proposed to participate in three distinct cellular processes: transcriptional elongation, polarized exocytosis, and formation of modified wobble uridines in tRNA. Uridine 242-250 Elongator subunit IKI3 Saccharomyces cerevisiae S288C 69-73 17576170-3 2007 Activation-induced cytidine deaminase (AID) converts cytidine to uridine to initiate the hypermutation process. Uridine 65-72 activation induced cytidine deaminase Homo sapiens 0-37 17576170-3 2007 Activation-induced cytidine deaminase (AID) converts cytidine to uridine to initiate the hypermutation process. Uridine 65-72 activation induced cytidine deaminase Homo sapiens 39-42 17706182-7 2007 The relative abilities of five human nucleoside transporters (hENT1/2, hCNT1/2/3 to bind the radiosensitizers were determined by quantifying their inhibition of uridine transport by recombinant transporters produced in yeast. Uridine 161-168 solute carrier family 29 member 1 (Augustine blood group) Homo sapiens 62-69 17706182-7 2007 The relative abilities of five human nucleoside transporters (hENT1/2, hCNT1/2/3 to bind the radiosensitizers were determined by quantifying their inhibition of uridine transport by recombinant transporters produced in yeast. Uridine 161-168 solute carrier family 28 member 1 Homo sapiens 71-80 17706182-10 2007 Beta-5-FAZR was a weak inhibitor of uridine transport relative to nonfluorinated 1-beta-D-(ribofuranosyl)-2-nitroimidazole (beta-AZR). Uridine 36-43 tubulin beta 4A class IVa Homo sapiens 0-11 16837649-1 2006 The Na(+)-dependent nucleoside transporter 2 (CNT2) mediates active transport of purine nucleosides and uridine as well as therapeutic nucleoside analogs. Uridine 104-111 solute carrier family 28 member 2 Rattus norvegicus 46-50 16837649-5 2006 Uridine and 2"-deoxyuridine analogs modified at the 5-position were substrates of rCNT2. Uridine 0-7 solute carrier family 28 member 2 Rattus norvegicus 82-87 17111347-4 2006 We show that uridine and ribose, the two defining features of RNA, are both necessary and sufficient for TLR7 stimulation, and that short single-stranded RNA (ssRNA) act as TLR7 agonists in a sequence-independent manner as long as they contain several uridines in close proximity. Uridine 13-20 toll like receptor 7 Homo sapiens 105-109 17056809-2 2006 In rats, dietary CDP-choline is rapidly metabolized into cytidine and choline; the cytidine is then readily converted to uridine, which enters the brain and, via conversion to UTP and CTP, increases brain levels of membrane phosphatides. Uridine 121-128 cut-like homeobox 1 Rattus norvegicus 17-20 17453413-7 2007 Only hCNT3 was also able to couple transport of uridine to uptake of H(+). Uridine 48-55 solute carrier family 28 member 3 Homo sapiens 5-10 17008930-2 2006 Precise insertion and deletion of hundreds of uridines is necessary to make full-length cytochrome c oxidase III (COXIII) mRNA. Uridine 46-54 mitochondrially encoded cytochrome c oxidase III Homo sapiens 88-112 17059404-0 2006 A mutation in an Arabidopsis ribose 5-phosphate isomerase reduces cellulose synthesis and is rescued by exogenous uridine. Uridine 114-121 Ribose 5-phosphate isomerase, type A protein Arabidopsis thaliana 29-57 17018299-1 2006 The Saccharomyces cerevisiae Elongator complex consisting of the six Elp1-Elp6 proteins has been proposed to participate in three distinct cellular processes: transcriptional elongation, polarized exocytosis, and formation of modified wobble uridines in tRNA. Uridine 242-250 Elongator subunit ELP6 Saccharomyces cerevisiae S288C 74-78 16769123-1 2006 The pyrimidines cytidine (as CTP) and uridine (which is converted to UTP and then CTP) contribute to brain phosphatidylcholine and phosphatidylethanolamine synthesis via the Kennedy pathway. Uridine 38-45 phosphate cytidylyltransferase 1A, choline Rattus norvegicus 82-85 16854981-6 2006 Fui1p-mediated transport of Urd was inhibited by analogs with modifications at C-5", but was not inhibited significantly by analogs with modifications at C-3", C-5, and N-3 or inversions of configuration at C-2" and C-3". Uridine 28-31 uridine permease Saccharomyces cerevisiae S288C 0-5 16769123-5 2006 CNT2 proteins, the high-affinity transporters for purines like adenosine as well as for uridine, have been found in cells comprising the BBB of rats. Uridine 88-95 solute carrier family 28 member 2 Rattus norvegicus 0-4 16839635-3 2006 Here, we investigated whether uridine, a pyrimidine nucleoside, could prevent the glucose deprivation-induced cytotoxicity in LPS+IFN-gamma-treated (immunostimulated) astrocytes. Uridine 30-37 interferon gamma Rattus norvegicus 130-139 16730994-4 2006 The second inhibitor molecule binds with the carboxyl group at the pyrimidine recognition site and the uridine moiety exploits interactions with RNase A residues Lys66, His119 and Asp121. Uridine 103-110 ribonuclease A family member 1, pancreatic Homo sapiens 145-152 16818232-2 2006 Since Py tracts are relatively poorly conserved in higher eukaryotes, U2AF(65) is faced with the problem of specifying uridine-rich sequences, yet tolerating a variety of nucleotide substitutions found in natural Py tracts. Uridine 119-126 U2 small nuclear RNA auxiliary factor 2 Homo sapiens 70-77 16871210-1 2006 Uridine at the first anticodon position (U34) of glutamate, lysine and glutamine transfer RNAs is universally modified by thiouridylase into 2-thiouridine (s2U34), which is crucial for precise translation by restricting codon-anticodon wobble during protein synthesis on the ribosome. Uridine 0-7 small nucleolar RNA, C/D box 34 Homo sapiens 41-44 16828706-9 2006 These results indicated that the previously reported mouse CNT2 is the wild-type one, and cytidine is transported mediated by the same recognition site on the CNT2 with uridine, and furthermore, cytidine analogues may be substrates for the transporter. Uridine 169-176 solute carrier family 28 (sodium-coupled nucleoside transporter), member 2 Mus musculus 59-63 16828706-9 2006 These results indicated that the previously reported mouse CNT2 is the wild-type one, and cytidine is transported mediated by the same recognition site on the CNT2 with uridine, and furthermore, cytidine analogues may be substrates for the transporter. Uridine 169-176 solute carrier family 28 (sodium-coupled nucleoside transporter), member 2 Mus musculus 159-163 16818232-3 2006 To better understand these apparently contradictory RNA binding characteristics, the X-ray structure of the U2AF(65) RNA binding domain bound to a Py tract composed of seven uridines has been determined at 2.5 A resolution. Uridine 174-182 U2 small nuclear RNA auxiliary factor 2 Homo sapiens 108-116 17016747-7 2006 ADP in the P2Y(12) receptor was located deeper inside the receptor in comparison to other subtypes, and the uridine moiety of UDP-glucose in the P2Y(14) receptor was located even deeper and shifted toward TM7. Uridine 108-115 purinergic receptor P2Y14 Homo sapiens 145-161 16636900-0 2006 Cytidine and uridine increase striatal CDP-choline levels without decreasing acetylcholine synthesis or release. Uridine 13-20 cut-like homeobox 1 Rattus norvegicus 39-42 17114947-1 2006 The pseudouridine synthase (Psi synthase) TruA catalyzes the conversion of uridine to pseudouridine at positions 38, 39 and/or 40 in the anticodon stem-loop (ASL) of tRNA. Uridine 10-17 tRNA pseudouridine(38-40) synthase TruA Thermus thermophilus HB8 42-46 16805952-7 2006 The cellular accumulation of L-valyl-ara-C was significantly reduced in the presence of uridine, p-aminohippurate, tetraethylammonium and small dipeptides, while it was not changed in the presence of L-valine and benzoic acid, suggesting that L-valyl-ara-C could interact with multiple uptake transporters, including peptide transporters, organic anion and cation transporters and nucleoside transporters, but might not interact with amino acid transporters. Uridine 88-95 ATP binding cassette subfamily C member 6 Homo sapiens 37-40 16784234-1 2006 Cytidine deaminase (CDA) is a zinc-dependent enzyme that catalyzes the deamination of cytidine or deoxycytidine to form uridine or deoxyuridine. Uridine 120-127 cytidine deaminase Mus musculus 0-18 16784234-1 2006 Cytidine deaminase (CDA) is a zinc-dependent enzyme that catalyzes the deamination of cytidine or deoxycytidine to form uridine or deoxyuridine. Uridine 120-127 cytidine deaminase Mus musculus 20-23 16711747-2 2006 Cytidine with water is efficiently converted to uridine with ammonia in the cleft of cytidine deaminase. Uridine 48-55 cytidine deaminase Homo sapiens 85-103