The PIR-International Protein Sequence Database.

abstract：:The E3 ubiquitin ligase HUWE1/Mule/ARF-BP1 plays an important role in integrating/coordinating diverse cellular processes such as DNA damage repair and apoptosis. A previous study has shown that HUWE1 is required for the early step of DNA damage-induced apoptosis, by targeting MCL-1 for proteasomal degradation. Howeve...

journal_title：Nucleic acids research

authors： Yi J,Lu G,Li L,Wang X,Cao L,Lin M,Zhang S,Shao G

更新日期：2015-05-19 00:00:00

abstract：:Major efforts are underway to elucidate the spatial distribution of ribosomal RNAs (rRNAs) in the ribosome. An especially informative approach is the identification of likely base-base tertiary interactions within the RNA by phylogenetic comparison. Herein evidence is presented for three heretofore unrecognized candid...

journal_title：Nucleic acids research

authors： Haselman T,Camp DG,Fox GE

更新日期：1989-03-25 00:00:00

abstract：:The mutation patterns at Cas9 targeted sites contain unique information regarding the nuclease activity and repair mechanisms in mammalian cells. However, analytical framework for extracting such information are lacking. Here, we present a novel computational platform called Rational InDel Meta-Analysis (RIMA) that en...

journal_title：Nucleic acids research

authors： Taheri-Ghahfarokhi A,Taylor BJM,Nitsch R,Lundin A,Cavallo AL,Madeyski-Bengtson K,Karlsson F,Clausen M,Hicks R,Mayr LM,Bohlooly-Y M,Maresca M

更新日期：2018-09-19 00:00:00

abstract：:Selection for amino acid affinity by elution of RNAs from tryptophan-Sepharose using free L-tryptophan evokes one sequence predominantly (K(D) = 12 microM), a symmetrical internal loop of 3 nt per side. Though we have also isolated larger sequences with affinity for tryptophan, successively squeezed selection in rando...

journal_title：Nucleic acids research

authors： Majerfeld I,Yarus M

更新日期：2005-09-25 00:00:00

abstract：:RNA can directly bind to purine-rich DNA via Hoogsteen base pairing, forming a DNA:RNA triple helical structure that anchors the RNA to specific sequences and allows guiding of transcription regulators to distinct genomic loci. To unravel the prevalence of DNA:RNA triplexes in living cells, we have established a fast ...

journal_title：Nucleic acids research

authors： Sentürk Cetin N,Kuo CC,Ribarska T,Li R,Costa IG,Grummt I

更新日期：2019-03-18 00:00:00

abstract：:JSNP is a repository of Japanese Single Nucleotide Polymorphism (SNP) data, begun in 2000 and developed through the Prime Minister's Millennium Project. The aim of this undertaking is to identify and collate up to 150 000 SNPs from the Japanese population, located in genes or in adjacent regions that might influence t...

journal_title：Nucleic acids research

authors： Hirakawa M,Tanaka T,Hashimoto Y,Kuroda M,Takagi T,Nakamura Y

更新日期：2002-01-01 00:00:00

abstract：:We characterized and purified a protein from rat liver which specifically binds to a DNA motif present in a liver-specific enhancer of the rat tyrosine aminotransferase (TAT) gene, when offered as single-stranded DNA. Binding is highly sequence-specific and coincides with a region known to be essential for function of...

journal_title：Nucleic acids research

authors： Jansen-Dürr P,Boshart M,Lupp B,Bosserhoff A,Frank RW,Schütz G

更新日期：1992-03-25 00:00:00

abstract：:The EcoRV DNA-(adenine-N(6))-methyltransferase (M.EcoRV) specifically modifies the first adenine residue within GATATC sequences. During catalysis, the enzyme flips its target base out of the DNA helix and binds it into a target base binding pocket which is formed in part by Lys16 and Tyr196. A cytosine residue is acc...

journal_title：Nucleic acids research

authors： Roth M,Jeltsch A

更新日期：2001-08-01 00:00:00

abstract：:All exchangeable protons in a short DNA helix, d(CG)3 sodium salt, have been studied by proton nuclear magnetic resonance. The cytidine and guanosine amino protons have been assigned for the first time. As a function of temperature the cytidine amino protons and the imino protons behave very similarly, their relaxatio...

journal_title：Nucleic acids research

authors： Fazakerley GV,van der Marel GA,van Boom JH,Guschlbauer W

更新日期：1984-11-12 00:00:00

abstract：:Non-structural protein 3 (NS3) of hepatitis C virus (HCV) has two distinct activities, protease and helicase, which are essential for HCV proliferation. In previous work, we obtained RNA aptamers (G9-I, II and III) which specifically bound the NS3 protease domain (DeltaNS3), efficiently inhibiting protease activity in...

journal_title：Nucleic acids research

authors： Nishikawa F,Kakiuchi N,Funaji K,Fukuda K,Sekiya S,Nishikawa S

更新日期：2003-04-01 00:00:00

abstract：:RNA editing of miRNAs, especially in the seed region, adds another layer to miRNA mediated gene regulation which can modify its targets, altering cellular signaling involved in important processes such as differentiation. In this study, we have explored the role of miRNA editing in CD4(+) T cell differentiation. CD4(+...

journal_title：Nucleic acids research

authors： Negi V,Paul D,Das S,Bajpai P,Singh S,Mukhopadhyay A,Agrawal A,Ghosh B

更新日期：2015-09-18 00:00:00

abstract：:The far upstream region of herpes simplex virus (HSV) immediate early (IE) gene 3 has previously been shown to increase gene expression in an enhancer-like manner, and to contain sequences which respond to stimulation of transcription by a virion polypeptide, Vmw65. To analyse the specific DNA sequences which mediate ...

journal_title：Nucleic acids research

authors： Bzik DJ,Preston CM

更新日期：1986-01-24 00:00:00

abstract：:Alternative first exons diversify the transcriptomes of eukaryotes by producing variants of the 5' Untranslated Regions (5'UTRs) and N-terminal coding sequences. Accurate transcriptome-wide detection of alternative first exons typically requires specialized experimental approaches that are designed to identify the 5' ...

journal_title：Nucleic acids research

authors： Qin Z,Stoilov P,Zhang X,Xing Y

更新日期：2018-05-04 00:00:00

abstract：:Comparative analysis of mutants using transfection is complicated by clones exhibiting variable levels of gene expression due to copy number differences and genomic position effects. Recombinase-mediated cassette exchange (RMCE) can overcome these problems by introducing the target gene into pre-determined chromosomal...

journal_title：Nucleic acids research

authors： Wong ET,Kolman JL,Li YC,Mesner LD,Hillen W,Berens C,Wahl GM

更新日期：2005-10-04 00:00:00

abstract：:R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field l...

journal_title：Nucleic acids research

authors： Vanquelef E,Simon S,Marquant G,Garcia E,Klimerak G,Delepine JC,Cieplak P,Dupradeau FY

更新日期：2011-07-01 00:00:00

abstract：:Phylogenetic analysis of Y-family DNA polymerases suggests that it can be subdivided into several discrete branches consisting of UmuC/DinB/Rev1/Rad30/Rad30A and Rad30B. The most diverse is the DinB family that is found in all three kingdoms of life. Searches of the complete genome of the crenarchaeon Sulfolobus solfa...

journal_title：Nucleic acids research

authors： Boudsocq F,Iwai S,Hanaoka F,Woodgate R

更新日期：2001-11-15 00:00:00

abstract：:The Gibbs Motif Sampler is a software package for locating common elements in collections of biopolymer sequences. In this paper we describe a new variation of the Gibbs Motif Sampler, the Gibbs Recursive Sampler, which has been developed specifically for locating multiple transcription factor binding sites for multip...

journal_title：Nucleic acids research

authors： Thompson W,Rouchka EC,Lawrence CE

更新日期：2003-07-01 00:00:00

abstract：:Translesional DNA synthesis past abasic sites proceeds with the preferential incorporation of dAMP opposite the lesion and, depending on the sequence context, one or two base deletions. High-resolution NMR spectroscopy and molecular dynamics simulations were used to determine the three-dimensional structure of a DNA h...

journal_title：Nucleic acids research

authors： Lin Z,Hung KN,Grollman AP,de los Santos C

更新日期：1998-05-15 00:00:00

abstract：:Bleomycin B(2)(BLM) in the presence of iron [Fe(II)] and O(2)catalyzes single-stranded (ss) and double-stranded (ds) cleavage of DNA. Electrospray ionization ion trap mass spectrometry was used to monitor these cleavage processes. Two duplex oligonucleotides containing an ethylene oxide tether between both strands wer...

journal_title：Nucleic acids research

authors： Harsch A,Marzilli LA,Bunt RC,Stubbe J,Vouros P

更新日期：2000-05-01 00:00:00

abstract：:An investigation of the mobility of short duplexes of DNA -octamers and decamers-on polyacrylamide gels is presented, showing that molecules containing less than one helical turn exhibit sequence dependent mobilities. Analysis of chains with different sequences indicates that any arrangement of two or more adjacent A....

journal_title：Nucleic acids research

authors： Chen JH,Seeman NC,Kallenbach NR

更新日期：1988-07-25 00:00:00

abstract：:S/MARt DB, the S/MAR transaction database, is a relational database covering scaffold/matrix attached regions (S/MARs) and nuclear matrix proteins that are involved in the chromosomal attachment to the nuclear scaffold. The data are mainly extracted from original publications, but a World Wide Web interface for direct...

journal_title：Nucleic acids research

authors： Liebich I,Bode J,Frisch M,Wingender E

更新日期：2002-01-01 00:00:00

abstract：:Ethidium causes the cleavage of DNA via a light and oxygen dependent process. Using covalently closed circular DNA as a substrate, the saturation kinetics and the dependence on superhelical density of the cleavage indicate that intercalated ethidium is mainly responsible for nicking DNA. Superoxide dismutase has littl...

journal_title：Nucleic acids research

authors： Deniss IS,Morgan AR

更新日期：1976-02-01 00:00:00

abstract：:Ribonucleotides are misincorporated into replicating DNA due to the similarity of deoxyribonucleotides and ribonucleotides, the high concentration of ribonucleotides in the nucleus and the imperfect accuracy of replicative DNA polymerases in choosing the base with the correct sugar. Embedded ribonucleotides change cer...

journal_title：Nucleic acids research

authors： Potenski CJ,Klein HL

更新日期：2014-01-01 00:00:00

abstract：:Gut-enriched Krüppel-like factor (GKLF or KLF4) is a pleiotropic (activating and repressive) transcription factor. This study characterizes the mechanisms of transactivation by GKLF. Using a GAL4 fusion assay, the activating domain of murine GKLF was localized to the 109 amino acid residues in the N-terminus. Site-dir...

journal_title：Nucleic acids research

authors： Geiman DE,Ton-That H,Johnson JM,Yang VW

更新日期：2000-03-01 00:00:00

abstract：:The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of the draft human genome, with the aim of accelerating genomics research through rapid open distribution of public data. Large amounts of raw data are thus transformed into knowledge, which...

journal_title：Nucleic acids research

authors： Zerbino DR,Achuthan P,Akanni W,Amode MR,Barrell D,Bhai J,Billis K,Cummins C,Gall A,Girón CG,Gil L,Gordon L,Haggerty L,Haskell E,Hourlier T,Izuogu OG,Janacek SH,Juettemann T,To JK,Laird MR,Lavidas I,Liu Z,Lovel

更新日期：2018-01-04 00:00:00

abstract：:With the improved secreted protein prediction approach and comprehensive data sources, including Swiss-Prot, TrEMBL, RefSeq, Ensembl and CBI-Gene, we have constructed secretomes of human, mouse and rat, with a total of 18 152 secreted proteins. All the entries are ranked according to the prediction confidence. They we...

journal_title：Nucleic acids research

authors： Chen Y,Zhang Y,Yin Y,Gao G,Li S,Jiang Y,Gu X,Luo J

更新日期：2005-01-01 00:00:00

abstract：:Transcription factors (TFs) and miRNAs are the most important dynamic regulators in the control of gene expression in multicellular organisms. These regulatory elements play crucial roles in development, cell cycling and cell signaling, and they have also been associated with many diseases. The Regulatory Network Anal...

journal_title：Nucleic acids research

authors： Bleda M,Medina I,Alonso R,De Maria A,Salavert F,Dopazo J

更新日期：2012-07-01 00:00:00

abstract：:Two enzymatic pathways are involved in the inhibitory effects of double-stranded (ds)RNA on protein synthesis in cell extracts derived from interferon-treated human fibroblasts or HeLa cells, an oligonucleotide polymerase that synthesizes (2'-5')An from ATP and a protein kinase that phosphorylates the alpha subunit of...

journal_title：Nucleic acids research

authors： Baglioni C,Minks MA,De Clercq E

更新日期：1981-10-10 00:00:00

abstract：:Interest in secondary metabolites such as RiPPs (ribosomally synthesized and posttranslationally modified peptides) is increasing worldwide. To facilitate the research in this field we have updated our mining web server. BAGEL4 is faster than its predecessor and is now fully independent from ORF-calling. Gene clusters...

journal_title：Nucleic acids research

authors： van Heel AJ,de Jong A,Song C,Viel JH,Kok J,Kuipers OP

更新日期：2018-07-02 00:00:00

abstract：:The Histone Database (HDB) is an annotated and searchable collection of all full-length sequences and structures of histone and non-histone proteins containing the histone fold motif. These sequences are both eukaryotic and archaeal in origin. Several new histone fold-containing proteins have been identified, includin...

journal_title：Nucleic acids research

authors： Sullivan SA,Aravind L,Makalowska I,Baxevanis AD,Landsman D

更新日期：2000-01-01 00:00:00