Bovine Genome Database: integrated tools for genome annotation and discovery.


:The Bovine Genome Database (BGD; strives to improve annotation of the bovine genome and to integrate the genome sequence with other genomics data. BGD includes GBrowse genome browsers, the Apollo Annotation Editor, a quantitative trait loci (QTL) viewer, BLAST databases and gene pages. Genome browsers, available for both scaffold and chromosome coordinate systems, display the bovine Official Gene Set (OGS), RefSeq and Ensembl gene models, non-coding RNA, repeats, pseudogenes, single-nucleotide polymorphism, markers, QTL and alignments to complementary DNAs, ESTs and protein homologs. The Bovine QTL viewer is connected to the BGD Chromosome GBrowse, allowing for the identification of candidate genes underlying QTL. The Apollo Annotation Editor connects directly to the BGD Chado database to provide researchers with remote access to gene evidence in a graphical interface that allows editing and creating new gene models. Researchers may upload their annotations to the BGD server for review and integration into the subsequent release of the OGS. Gene pages display information for individual OGS gene models, including gene structure, transcript variants, functional descriptions, gene symbols, Gene Ontology terms, annotator comments and links to National Center for Biotechnology Information and Ensembl. Each gene page is linked to a wiki page to allow input from the research community.


Nucleic Acids Res


Nucleic acids research


Childers CP,Reese JT,Sundaram JP,Vile DC,Dickens CM,Childs KL,Salih H,Bennett AK,Hagen DE,Adelson DL,Elsik CG




Has Abstract


2011-01-01 00:00:00




Database issue










  • Structure of transfer RNA by carbon NMR: resolution of single carbon resonances from 13C-enriched, purified species.

    abstract::Methyl carbon-13 NMR spectra of purified tRNA species are presented for the first time. In addition, these spectra of tRNA species specific for phenylalanine, tyrosine, and cysteine exhibited the first resolution of single methyl carbon resonances. Carbon-13 enriched methyl groups of ribothymidine (T) and 7-methylguan...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Agris PF,Schmidt PG

    更新日期:1980-05-10 00:00:00

  • Correction of the consequences of mitochondrial 3243A>G mutation in the MT-TL1 gene causing the MELAS syndrome by tRNA import into mitochondria.

    abstract::Mutations in human mitochondrial DNA are often associated with incurable human neuromuscular diseases. Among these mutations, an important number have been identified in tRNA genes, including 29 in the gene MT-TL1 coding for the tRNA(Leu(UUR)). The m.3243A>G mutation was described as the major cause of the MELAS syndr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Karicheva OZ,Kolesnikova OA,Schirtz T,Vysokikh MY,Mager-Heckel AM,Lombès A,Boucheham A,Krasheninnikov IA,Martin RP,Entelis N,Tarassov I

    更新日期:2011-10-01 00:00:00

  • Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB.

    abstract::Successful development of biological databases requires accommodation of the burgeoning amounts of data from high-throughput genomics pipelines. As the volume of curated data in Animal QTLdb ( increases exponentially, the resulting challenges must be met with rapid infrastructure dev...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hu ZL,Park CA,Reecy JM

    更新日期:2019-01-08 00:00:00

  • A manganese-dependent ribozyme in the 3'-untranslated region of Xenopus Vg1 mRNA.

    abstract::The smallest catalytic RNA identified to date is a manganese-dependent ribozyme that requires only a complex between GAAA and UUU to effect site-specific cleavage. We show here that this ribozyme occurs naturally in the 3'-UTR of Vg1 and beta-actin mRNAs. In accord with earlier studies with model RNAs, cleavage occurs...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kolev NG,Hartland EI,Huber PW

    更新日期:2008-10-01 00:00:00

  • Multitarget-ribozyme directed to cleave at up to nine highly conserved HIV-1 env RNA regions inhibits HIV-1 replication--potential effectiveness against most presently sequenced HIV-1 isolates.

    abstract::Several mono-, di-, tetra-, penta- and nonaribozymes were developed. These multitarget-ribozymes were targeted to cleave HIV-1 env RNA at up to nine different conserved sites. Each multitarget-ribozyme consisted of a chain of up to nine hammerhead motifs, each flanked by a different targeting sequence. The multitarget...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chen CJ,Banerjea AC,Harmison GG,Haglund K,Schubert M

    更新日期:1992-09-11 00:00:00

  • PAH Mutation Analysis Consortium Database: 1997. Prototype for relational locus-specific mutation databases.

    abstract::PAHdb ( ) is a curated relational database (Fig. 1) of nucleotide variation in the human PAH cDNA (GenBank U49897). Among 328 different mutations by state (Fig. 2) the majority are rare mutations causing hyperphenylalaninemia (HPA) (OMIM 261600), the remainder are polymorphic variants without...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Nowacki PM,Byck S,Prevost L,Scriver CR

    更新日期:1998-01-01 00:00:00

  • Functional characterization of Rad18 domains for Rad6, ubiquitin, DNA binding and PCNA modification.

    abstract::Rad18 is a ubiquitin E3 ligase that monoubiquitinates PCNA on stalled replications forks. This allows recruitment of damage-tolerant polymerases for damage bypass and DNA repair. In this activity, the Rad18 protein has to interact with Rad6, the E2 ubiquitin-conjugating enzyme, ubiquitin, PCNA and DNA. Here we analyze...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Notenboom V,Hibbert RG,van Rossum-Fikkert SE,Olsen JV,Mann M,Sixma TK

    更新日期:2007-01-01 00:00:00

  • Vectors for P element-mediated gene transfer in Drosophila.

    abstract::We have constructed and tested several new vectors for P element-mediated gene transfer. These vectors contain restriction sites for cloning a wide variety of DNA fragments within a small, non-autonomous P element and can be used to efficiently transduce microinjected DNA sequences into the germ line chromosomes of D....

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rubin GM,Spradling AC

    更新日期:1983-09-24 00:00:00

  • Defective in vitro binding of histidyl-transfer ribonucleic acid to feedback resistant phosphoribosyl transferase of Salmonella typhimurium.

    abstract::We previously proposed that the first enzyme for histidine biosynthesis in Salmonellatyphimurium plays a role in regulating expression of the histidine operon and that in order to play this role the enzyme must form a complex with histidyl-tRNA. Among the many observations that led to these conclusions were 1) that re...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Smith O,Meyers MM,Vogel T,Deeley RD,Goldberger R

    更新日期:1974-07-01 00:00:00

  • 3' processing of pre-mRNA plays a major role in proliferation-dependent regulation of histone gene expression.

    abstract::A short histone-like fusion RNA, generated when the RNA 3' processing signal from a mouse histone H4 gene is inserted into a heterologous transcription unit, becomes correctly down-regulated in G1-arrested cells of a temperature-sensitive mouse mastocytoma cell cycle mutant (21-Tb; Stauber et al., EMBO J. 5, 3297-3303...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Stauber C,Schümperli D

    更新日期:1988-10-25 00:00:00

  • The 5' terminal oligopyrimidine tract confers translational control on TOP mRNAs in a cell type- and sequence context-dependent manner.

    abstract::TOP mRNAs are vertebrate transcripts which contain a 5'terminal oligopyrimidine tract (5'TOP), encode for ribosomal proteins and elongation factors 1alpha and 2, and are candidates for growth-dependent translational control mediated through their 5'TOP. In the present study we show that elongation factor 2 (EF2) mRNA ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Avni D,Biberman Y,Meyuhas O

    更新日期:1997-03-01 00:00:00

  • A designed RNA selection: establishment of a stable complex between a target and selectant RNA via two coordinated interactions.

    abstract::In this paper, we describe a new method for selecting RNA aptamers that cooperatively bind to two specific sites within a target RNA. We designed a selection system in which two RNAs, a target RNA and a RNA pool, were assembled by employing a pre-organized GAAA tetraloop-11-nt receptor interaction. This allows us to s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Shiohara T,Saito H,Inoue T

    更新日期:2009-02-01 00:00:00

  • DNA modification by sulfur: analysis of the sequence recognition specificity surrounding the modification sites.

    abstract::The Dnd (DNA degradation) phenotype, reflecting a novel DNA modification by sulfur in Streptomyces lividans 1326, was strongly aggravated when one (dndB) of the five genes (dndABCDE) controlling it was mutated. Electrophoretic banding patterns of a plasmid (pHZ209), reflecting DNA degradation, displayed a clear change...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Liang J,Wang Z,He X,Li J,Zhou X,Deng Z

    更新日期:2007-01-01 00:00:00

  • Isolation and characterization of cloned human fetal globin genes.

    abstract::Three clones containing both the human G gamma and A gamma globlin genes have been isolated and characterized from a library of DNA fragments generated by partial Eco RI digestion of cellular DNA using charon 4A phage as vector. Two of the clones (NY 2 and 3) are identical and have an insert of 14.0 kb. The third clon...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ramirez F,Burns AL,Mears JG,Spence S,Starkman D,Bank A

    更新日期:1979-11-10 00:00:00

  • Engineering a portable riboswitch-LacP hybrid device for two-way gene regulation.

    abstract::Riboswitches are RNA-based regulatory devices that mediate ligand-dependent control of gene expression. However, there has been limited success in rationally designing riboswitches. Moreover, most previous riboswitches are confined to a particular gene and only perform one-way regulation. Here, we used a library scree...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Jin Y,Huang JD

    更新日期:2011-10-01 00:00:00

  • Multiple whole genome alignments and novel biomedical applications at the VISTA portal.

    abstract::The VISTA portal for comparative genomics is designed to give biomedical scientists a unified set of tools to lead them from the raw DNA sequences through the alignment and annotation to the visualization of the results. The VISTA portal also hosts the alignments of a number of genomes computed by our group, allowing ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Brudno M,Poliakov A,Minovitsky S,Ratnere I,Dubchak I

    更新日期:2007-07-01 00:00:00

  • Messenger RNA abundance and lifetime: a correlation in Drosophila cells but not in HeLa.

    abstract::Messenger RNA in eukaryotes is comprised of several abundance classes. Also, the decay of these unstable molecules shows at least two very different lifetimes. Two independent techniques are used here to examine the relation between message abundance and lifetime in cell lines from very different organisms. The method...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lenk R,Herman R,Penman S

    更新日期:1978-08-01 00:00:00

  • MAVL/StickWRLD for protein: visualizing protein sequence families to detect non-consensus features.

    abstract::A fundamental problem with applying Consensus, Weight-Matrix or hidden Markov models as search tools for biosequences is that there is no way to know, from the model, if the modeled sequences display any dependencies between positional identities. In some instances, these dependencies are crucial in correctly acceptin...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ray WC

    更新日期:2005-07-01 00:00:00

  • High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions.

    abstract::The emergence of massively parallel sequencing technology has revolutionized microbial profiling, allowing the unprecedented comparison of microbial diversity across time and space in a wide range of host-associated and environmental ecosystems. Although the high-throughput nature of such methods enables the detection...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Amir A,Zeisel A,Zuk O,Elgart M,Stern S,Shamir O,Turnbaugh PJ,Soen Y,Shental N

    更新日期:2013-12-01 00:00:00

  • Peripheral re-localization of constitutive heterochromatin advances its replication timing and impairs maintenance of silencing marks.

    abstract::The replication of the genome is a highly organized process, both spatially and temporally. Although a lot is known on the composition of the basic replication machinery, how its activity is regulated is mostly unknown. Several chromatin properties have been proposed as regulators, but a potential role of the nuclear ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Heinz KS,Casas-Delucchi CS,Török T,Cmarko D,Rapp A,Raska I,Cardoso MC

    更新日期:2018-07-06 00:00:00

  • Interaction between RECQL4 and OGG1 promotes repair of oxidative base lesion 8-oxoG and is regulated by SIRT1 deacetylase.

    abstract::OGG1 initiated base excision repair (BER) is the major pathway for repair of oxidative DNA base damage 8-oxoguanine (8-oxoG). Here, we report that RECQL4 DNA helicase, deficient in the cancer-prone and premature aging Rothmund-Thomson syndrome, physically and functionally interacts with OGG1. RECQL4 promotes catalytic...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Duan S,Han X,Akbari M,Croteau DL,Rasmussen LJ,Bohr VA

    更新日期:2020-07-09 00:00:00

  • Patterns in interspecies similarity correlate with nucleotide composition in mammalian 3'UTRs.

    abstract::Post-transcriptional regulation and the formation of mRNA 3' ends are crucial for gene expression in eukaryotes. Interspecies conservation of many sequences within 3'UTRs reveals selective constraint due to similar function. To study the pattern of conservation within 3'UTRs, we compiled and aligned 50 sets of complet...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Shabalina SA,Ogurtsov AY,Lipman DJ,Kondrashov AS

    更新日期:2003-09-15 00:00:00

  • Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules.

    abstract::Data produced with short-read sequencing technologies result in ambiguous haplotyping and a limited capacity to investigate the full repertoire of biologically relevant forms of genetic variation. The notion of haplotype-resolved sequencing data has recently gained traction to reduce this unwanted ambiguity and enable...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Redin D,Borgström E,He M,Aghelpasand H,Käller M,Ahmadian A

    更新日期:2017-07-27 00:00:00

  • Identification of a homeobox-containing gene located between lin-45 and unc-24 on chromosome IV in the nematode Caenorhabditis elegans.

    abstract::Using two primers corresponding to helix 1 and helix 3 regions in the homeodomain, we subjected genomic DNA from Caenorhabditis elegans to amplification by the polymerase chain reaction. Sequence analysis of the amplified products revealed a new homeobox-containing gene, designated ceh-19. This gene was located betwee...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Naito M,Kohara Y,Kurosawa Y

    更新日期:1992-06-25 00:00:00

  • Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers.

    abstract::We describe here a novel method for integrating gene and miRNA expression profiles in cancer using feed-forward loops (FFLs) consisting of transcription factors (TFs), miRNAs and their common target genes. The dChip-GemiNI (Gene and miRNA Network-based Integration) method statistically ranks computationally predicted ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Yan Z,Shah PK,Amin SB,Samur MK,Huang N,Wang X,Misra V,Ji H,Gabuzda D,Li C

    更新日期:2012-09-01 00:00:00

  • Characterisation of membrane oligonucleotide-binding proteins and oligonucleotide uptake in keratinocytes.

    abstract::Inadequate cellular compartmentalisation of plasmid DNA and antisense oligodeoxynucleotides (ODNs) is generally considered as a major limitation in their use. In this study, an approach combining in situ visual-isation of rhodamine-labelled ODNs and affinity modification of proteins by radiolabelled-alkylating ODN der...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Laktionov PP,Dazard JE,Vives E,Rykova EY,Piette J,Vlassov VV,Lebleu B

    更新日期:1999-06-01 00:00:00

  • Energy-structure correlations of plasmid DNA in different topological forms.

    abstract::Differential scanning microcalorimetry (DSC), UV absorption and circular dichroism (CD) have been used to study structure and stability of linear (lin), open circular (oc), supercoiled (cd) and relaxed circular duplex (rd) DNA and calf thymus (CT) DNA. Investigations were made in low salt buffer and in the presence of...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Thumm W,Seidl A,Hinz HJ

    更新日期:1988-12-23 00:00:00

  • Elements at the 5' end of Xist harbor SPEN-independent transcriptional antiterminator activity.

    abstract::The Xist lncRNA requires Repeat A, a conserved RNA element located in its 5' end, to induce gene silencing during X-chromosome inactivation. Intriguingly, Repeat A is also required for production of Xist. While silencing by Repeat A requires the protein SPEN, how Repeat A promotes Xist production remains unclear. We r...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Trotman JB,Lee DM,Cherney RE,Kim SO,Inoue K,Schertzer MD,Bischoff SR,Cowley DO,Calabrese JM

    更新日期:2020-10-09 00:00:00

  • Molecular structures of two new anti-HIV nucleoside analogs: 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl)adenine and 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl)hypoxanthine.

    abstract::The x-ray crystal structures of two new anti-HIV compounds, 9-(2,3-dideoxy-2-fluoro-beta-D-threo-pentofuranosyl)adenine (2'-F-dd-araA) and 9-(2,3-dideoxy-2-fluoro-beta-D-threo- pentofuranosyl)hypoxanthine (2'-F-dd-aral), have been determined at two temperatures. Both crystals are in the space group P2(1)2(1)2(1), and ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Liaw YC,Gao YG,Marquez VE,Wang AH

    更新日期:1992-02-11 00:00:00

  • Cloning and expression of the Staphylococcus aureus protein A gene in Escherichia coli.

    abstract::A gene bank of Staphylococcus aureus strain Cowan I was established using an E. coli HB101/pBR327 host-vector system. Recombinants expressing staphylococcal protein A (SPA) were detected using an IgG-binding assay. A 3.2 Kb DNA fragment directing the synthesis of SPA in E. coli was identified. SPA produced by E. coli ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Duggleby CJ,Jones SA

    更新日期:1983-05-25 00:00:00