Rfam: annotating non-coding RNAs in complete genomes.


:Rfam is a comprehensive collection of non-coding RNA (ncRNA) families, represented by multiple sequence alignments and profile stochastic context-free grammars. Rfam aims to facilitate the identification and classification of new members of known sequence families, and distributes annotation of ncRNAs in over 200 complete genome sequences. The data provide the first glimpses of conservation of multiple ncRNA families across a wide taxonomic range. A small number of large families are essential in all three kingdoms of life, with large numbers of smaller families specific to certain taxa. Recent improvements in the database are discussed, together with challenges for the future. Rfam is available on the Web at http://www.sanger.ac.uk/Software/Rfam/ and http://rfam.wustl.edu/.


Nucleic Acids Res


Nucleic acids research


Griffiths-Jones S,Moxon S,Marshall M,Khanna A,Eddy SR,Bateman A





Has Abstract


2005-01-01 00:00:00




Database issue










  • A deafness-associated tRNA mutation caused pleiotropic effects on the m1G37 modification, processing, stability and aminoacylation of tRNAIle and mitochondrial translation.

    abstract::Defects in the posttranscriptional modifications of mitochondrial tRNAs have been linked to human diseases, but their pathophysiology remains elusive. In this report, we investigated the molecular mechanism underlying a deafness-associated tRNAIle 4295A>G mutation affecting a highly conserved adenosine at position 37,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Meng F,Zhou M,Xiao Y,Mao X,Zheng J,Lin J,Lin T,Ye Z,Cang X,Fu Y,Wang M,Guan MX

    更新日期:2021-01-25 00:00:00

  • The processing of wild type and mutant forms of rat nuclear pre-tRNA(Lys) by the homologous RNase P.

    abstract::The 5' processing of rat pre-tRNA(Lys) and a series of mutant derivatives by rat cytosolic RNase P was examined. In standard, non-kinetic assays, mutant precursors synthesized in vitro with 5' leader sequences of 10, 17, 24, 25, and 46 nucleotides were processed to approximately equal levels and yielded precisely clea...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Paisley TE,Van Tuyle GC

    更新日期:1994-08-25 00:00:00

  • RNABindR: a server for analyzing and predicting RNA-binding sites in proteins.

    abstract::Understanding interactions between proteins and RNA is key to deciphering the mechanisms of many important biological processes. Here we describe RNABindR, a web-based server that identifies and displays RNA-binding residues in known protein-RNA complexes and predicts RNA-binding residues in proteins of unknown struct...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Terribilini M,Sander JD,Lee JH,Zaback P,Jernigan RL,Honavar V,Dobbs D

    更新日期:2007-07-01 00:00:00

  • 20-Hydroxyecdysone increases levels of transient gene expression in transfected Drosophila cells.

    abstract::Methods for increasing the transient level of expression of transfected DNA in cultured Drosophila cells have been examined. Here we show that cells exposed to the steroid hormone 20-hydroxyecdysone for 48h prior to transfection show an 4 to 5 fold increase in the levels of expression of transfected DNA. By analysis, ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sinclair JH,Bryant LA

    更新日期:1987-11-25 00:00:00

  • Cloning and functional analysis of spliced isoforms of human nuclear factor I-X: interference with transcriptional activation by NFI/CTF in a cell-type specific manner.

    abstract::Previous studies of the epithelial specificity of the human papillomavirus type 16 (HPV-16) enhancer pointed out an important role of nuclear factor I (NFI). In epithelial cells, NFI proteins are derived from the NFI-C gene and referred to as NFI/CTF. In contrast, fibroblasts, where the enhancer is inactive, express h...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Apt D,Liu Y,Bernard HU

    更新日期:1994-09-25 00:00:00

  • ATPase activity of the UvrA and UvrAB protein complexes of the Escherichia coli UvrABC endonuclease.

    abstract::We have analyzed the ATPase activity exhibited by the UvrABC DNA repair complex. The UvrA protein is an ATPase whose lack of DNA dependence may be related to the ATP induced monomer-dimer transitions. ATP induced dimerization may be responsible for the enhanced DNA binding activity observed in the presence of ATP. Alt...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Oh EY,Claassen L,Thiagalingam S,Mazur S,Grossman L

    更新日期:1989-06-12 00:00:00

  • CTC1-mediated C-strand fill-in is an essential step in telomere length maintenance.

    abstract::To prevent progressive telomere shortening as a result of conventional DNA replication, new telomeric DNA must be added onto the chromosome end. The de novo DNA synthesis involves elongation of the G-rich strand of the telomere by telomerase. In human cells, the CST complex (CTC1-STN1-TEN1) also functions in telomere ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Feng X,Hsu SJ,Kasbek C,Chaiken M,Price CM

    更新日期:2017-05-05 00:00:00

  • Error-free and error-prone lesion bypass by human DNA polymerase kappa in vitro.

    abstract::Error-free lesion bypass and error-prone lesion bypass are important cellular responses to DNA damage during replication, both of which require a DNA polymerase (Pol). To identify lesion bypass DNA polymerases, we have purified human Polkappa encoded by the DINB1 gene and examined its response to damaged DNA templates...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhang Y,Yuan F,Wu X,Wang M,Rechkoblit O,Taylor JS,Geacintov NE,Wang Z

    更新日期:2000-11-01 00:00:00

  • Global transcript structure resolution of high gene density genomes through multi-platform data integration.

    abstract::Annotation of herpesvirus genomes has traditionally been undertaken through the detection of open reading frames and other genomic motifs, supplemented with sequencing of individual cDNAs. Second generation sequencing and high-density microarray studies have revealed vastly greater herpesvirus transcriptome complexity...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: O'Grady T,Wang X,Höner Zu Bentrup K,Baddoo M,Concha M,Flemington EK

    更新日期:2016-10-14 00:00:00

  • Structure of replication origin of the Escherichia coli K-12 chromosome: the presence of spacer sequences in the ori region carrying information for autonomous replication.

    abstract::The replication origin region of the Escherichia coli K-12 chromosome has been cloned, and a region of 245 base-pairs has been shown to contain all the information for autonomous replication (defined ori). In order to obtain further information on the sequence organization in the defined ori stretch, various types of ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Asada K,Sugimoto K,Oka A,Takanami M,Hirota Y

    更新日期:1982-06-25 00:00:00

  • The role of GTP in transient splitting of 70S ribosomes by RRF (ribosome recycling factor) and EF-G (elongation factor G).

    abstract::Ribosome recycling factor (RRF), elongation factor G (EF-G) and GTP split 70S ribosomes into subunits. Here, we demonstrated that the splitting was transient and the exhaustion of GTP resulted in re-association of the split subunits into 70S ribosomes unless IF3 (initiation factor 3) was present. However, the splittin...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hirokawa G,Iwakura N,Kaji A,Kaji H

    更新日期:2008-12-01 00:00:00

  • Bacterial regulatory networks are extremely flexible in evolution.

    abstract::Over millions of years the structure and complexity of the transcriptional regulatory network (TRN) in bacteria has changed, reorganized and enabled them to adapt to almost every environmental niche on earth. In order to understand the plasticity of TRNs in bacteria, we studied the conservation of currently known TRNs...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lozada-Chávez I,Janga SC,Collado-Vides J

    更新日期:2006-07-13 00:00:00

  • MGAlignIt: A web service for the alignment of mRNA/EST and genomic sequences.

    abstract::Splicing is a biological phenomenon that removes the non-coding sequence from the transcripts to produce a mature transcript suitable for translation. To study this phenomenon, information on the intron-exon arrangement of a gene is essential, usually obtained by aligning mRNA/EST sequences to their cognate genomic se...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lee BT,Tan TW,Ranganathan S

    更新日期:2003-07-01 00:00:00

  • DNA associated with nucleosomes in plants.

    abstract::50 to 55% of tobacco and barley nuclear DNA is accessible to micrococcal endonuclease digestion. The DNA fragments resulting from a mild endonuclease treatment are multiples of a basic unit of 194 +/- 6 base pairs in tobacco and 195 +/- 6 base pairs in barley. After extensive digestion, a DNA fragment of approximately...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Philipps G,Gigot C

    更新日期:1977-10-01 00:00:00

  • TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation.

    abstract::Three databases that provide data on transcriptional regulation are described. TRANSFAC is a database on transcription factors and their DNA binding sites. TRRD (Transcription Regulatory Region Database) collects information about complete regulatory regions, their regulation properties and architecture. COMPEL compri...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Wingender E,Kel AE,Kel OV,Karas H,Heinemeyer T,Dietze P,Knüppel R,Romaschenko AG,Kolchanov NA

    更新日期:1997-01-01 00:00:00

  • Misincorporation of dAMP opposite 2-hydroxyadenine, an oxidative form of adenine.

    abstract::Nucleotide incorporation opposite an oxidative form of adenine, 2-hydroxyadenine (2-OH-Ade) was investigated. When a primed template with 2-OH-Ade was treated with an exonuclease-deficient Klenow fragment of Escherichia coli DNA polymerase I (KFexo-), recombinant rat DNA polymerase beta (pol beta) or calf thymus DNA p...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kamiya H,Ueda T,Ohgi T,Matsukage A,Kasai H

    更新日期:1995-03-11 00:00:00

  • Intermediates in plasmid pT181 DNA replication.

    abstract::Staphylococcus aureus plasmid pT181 is thought to replicate via an asymmetric rolling-circle mechanism. By studying pulse labeled replicative intermediates, here we report that pT181 replication involves: (1) a post-replicative hypersupercoiled monomer and (2) a partially replicated intermediate which lacks superhelic...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Majumder S,Novick RP

    更新日期:1988-04-11 00:00:00

  • DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association.

    abstract::microRNAs (miRNAs) are small endogenous RNA molecules that are implicated in many biological processes through post-transcriptional regulation of gene expression. The DIANA-microT Web server provides a user-friendly interface for comprehensive computational analysis of miRNA targets in human and mouse. The server has ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Maragkakis M,Vergoulis T,Alexiou P,Reczko M,Plomaritou K,Gousis M,Kourtis K,Koziris N,Dalamagas T,Hatzigeorgiou AG

    更新日期:2011-07-01 00:00:00

  • Relief of triple-helix-mediated promoter inhibition by elongating RNA polymerases.

    abstract::We have characterized triple-helix-mediated inhibition of an artificial bacteriophage promoter with respect to relief of inhibition by incoming RNA polymerases that initiate upstream or downstream from the operator sequence. Whereas oligonucleotide-directed triple-helix formation inhibits the test promoter, promoter a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Skoog JU,Maher LJ 3rd

    更新日期:1993-08-25 00:00:00

  • The virtues of self-binding: high sequence specificity for RNA cleavage by self-processed hammerhead ribozymes.

    abstract::Naturally occurring hammerhead ribozymes are produced by rolling circle replication followed by self-cleavage. This results in monomer-length catalytic RNAs which have self-complementary sequences that can occupy their trans -binding domains and potentially block their ability to cleave other RNA strands. Here we show...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ohmichi T,Kool ET

    更新日期:2000-02-01 00:00:00

  • Ensembl 2018.

    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

    pub_type: 杂志文章


    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

  • A simplified method of generating transgenic Xenopus.

    abstract::Currently transgenic frog embryos are generated using restriction-enzyme-mediated integration (REMI) on decondensed sperm nuclei followed by nuclear transplantation into unfertilized eggs. We have developed a simplified version of this protocol that has the potential to increase the numbers of normally developing tran...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sparrow DB,Latinkic B,Mohun TJ

    更新日期:2000-02-15 00:00:00

  • Delineation of the high-affinity single-stranded telomeric DNA-binding domain of Saccharomyces cerevisiae Cdc13.

    abstract::Cdc13 is an essential protein from Saccharomyces cerevisiae that caps telomeres by protecting the C-rich telomeric DNA strand from degradation and facilitates telomeric DNA replication by telomerase. In vitro, Cdc13 binds TG-rich single-stranded telomeric DNA with high affinity and specificity. A previously identified...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Anderson EM,Halsey WA,Wuttke DS

    更新日期:2002-10-01 00:00:00

  • Post-transcriptional modification of the poly(A) length of galactose-1-phosphate uridyl transferase mRNA in Saccharomyces cerevisiae.

    abstract::Thermal elution poly(U)-Sepharose chromatography was utilized to fractionate yeast mRNA based on poly(A) size. Analysis of the in vitro translation products of the fractionated RNAs in a wheat-embryo cell-free protein synthesis system shows a heterogeneous but equal distribution of these abundant translatable mRNAs in...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Saunders CA,Bostian KA,Halvorson HO

    更新日期:1980-09-11 00:00:00

  • MyoD1 promoter autoregulation is mediated by two proximal E-boxes.

    abstract::We show that in mouse myoblasts the MyoD1 promoter is highly stimulated by MyoD1 expression, suggesting that it is controlled by a positive feedback loop. Using deletion and mutation analyses, we identified the targets for MyoD1 promoter autoregulation as the two proximal E-boxes located close to the MyoD1 core promot...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zingg JM,Pedraza-Alva G,Jost JP

    更新日期:1994-06-25 00:00:00

  • PCR performance of the B-type DNA polymerase from the thermophilic euryarchaeon Thermococcus aggregans improved by mutations in the Y-GG/A motif.

    abstract::The effect of mutations in the highly conserved Y-GG/A motif of B-type DNA polymerases was studied in the DNA polymerase from the hyperthermophilic euryarchaeon Thermococcus aggregans. This motif plays a critical role in the balance between the synthesis and degradation of the DNA chain. Five different mutations of th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Böhlke K,Pisani FM,Vorgias CE,Frey B,Sobek H,Rossi M,Antranikian G

    更新日期:2000-10-15 00:00:00

  • DNA synthesis is initiated at two positions within the origin of replication of plasmid R1162.

    abstract::DNA synthesis of broad host-range plasmid R1162 is initiated from two positions, flanking a large (40 bp stem, 40 bp loop) inverted repeat. Each start-point is located within a highly conserved, but oppositely oriented, 10 base-pair sequence. Synthesis from the two positions converges within the intervening inverted r...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lin LS,Meyer RJ

    更新日期:1987-10-26 00:00:00

  • ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis.

    abstract::Publicly available database of co-expressed gene sets would be a valuable tool for a wide variety of experimental designs, including targeting of genes for functional identification or for regulatory investigation. Here, we report the construction of an Arabidopsis thaliana trans-factor and cis-element prediction data...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Obayashi T,Kinoshita K,Nakai K,Shibaoka M,Hayashi S,Saeki M,Shibata D,Saito K,Ohta H

    更新日期:2007-01-01 00:00:00

  • Monomolecular G-quadruplex structures with inversion of polarity sites: new topologies and potentiality.

    abstract::In this paper, we report investigations, based on circular dichroism, nuclear magnetic resonance spectroscopy and electrophoresis methods, on three oligonucleotide sequences, each containing one 3'-3' and two 5'-5' inversion of polarity sites, and four G-runs with a variable number of residues, namely two, three and f...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Virgilio A,Russo A,Amato T,Russo G,Mayol L,Esposito V,Galeone A

    更新日期:2017-08-21 00:00:00

  • High efficiency family shuffling based on multi-step PCR and in vivo DNA recombination in yeast: statistical and functional analysis of a combinatorial library between human cytochrome P450 1A1 and 1A2.

    abstract::The design of a family shuffling strategy (CLERY: Combinatorial Libraries Enhanced by Recombination in Yeast) associating PCR-based and in vivo recombination and expression in yeast is described. This strategy was tested using human cytochrome P450 CYP1A1 and CYP1A2 as templates, which share 74% nucleotide sequence id...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Abécassis V,Pompon D,Truan G

    更新日期:2000-10-15 00:00:00