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TransTerm, the translational signal database, extended to include full coding sequences and untranslated regions

NUCLEIC ACIDS RESEARCH 1999年第1期27卷 293-294页

作者： Dalphin, ME Stockwell, PA Tate, WP Brown, CM Univ Otago Dept Biochem Dunedin New Zealand

TransTerm is a database of mRNA sequences and parameters useful for detecting translational control signals in general. TransTerm-98 has been expanded beyond previous years to include full coding sequences and UTRs, while retaining the original small contexts about the coding sequence start- and stop-codons. The database contains more than 130 000 non-redundant coding sequences with associated untranslated regions (UTRs) from over 450 species. This includes the complete genomes of 12 prokaryotic and one eukaryotic organism. Several coding sequence parameters are available: coding sequence length, Nc, GC3 and, when it is computable. Codon Adaptation index (CAI). Codon usage tables and summaries of start- and stop-codon contexts are also included. TransTerm-98 has both a relational database form with a WWW interface and a flatfile format, also available by Internet browser. TransTerm is available at: http://***:800/Transterm/***.

关键词： .format codon UTRs includes coding sequence relational translational signal database TransTerm full coding

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Polytime coding as a means of pulse compression

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IEEE TRANSACTIONS ON AEROSPACE AND ELECTRONIC SYSTEMS 1999年第2期35卷 716-721页

作者： Fielding, JE Radian Int Austin TX 78720 USA

A set of code sequences is proposed for radar applications in which all phase steps are equal and the time duration of each phase state is varied in order to properly approximate either a stepped-RE waveform or a linear FM waveform, Since these proposed waveforms have varying time durations at each phase state, they are referred to as "Polytime" codes. Polytime code sequences have the advantage that arbitrary time-bandwidth waveforms can be generated with a few phase states. Of particular interest are cases where phase is quantized into two states (i.e., 0 degrees and 180 degrees).

关键词： modulation coding phase coding pulse compression radar signal processing sequential codes Doppler tolerance Polytime coding arbitrary time-bandwidth waveforms code sequences linear FM waveform phase quantization radar applications stepp Radar signal processing phase coding waveforms sequential codes Pulse compression STATE(PHASE) Radar applications coding sequence modulation coding

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Total number of coding open reading frames in the yeast genome

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YEAST 1999年第11期15卷 1031-1034页

作者： Kowalczuk, M Mackiewicz, P Gierlik, A Dudek, MR Cebrat, S Univ Wroclaw Inst Microbiol PL-51148 Wroclaw Poland Univ Wroclaw Inst Theoret Phys PL-50204 Wroclaw Poland

At the end of 1996 we approximated the total number of protein coding ORFs in the Saccharomyces cerevisiae genome, based on their properties, as 4700-4800. The number is much smaller than the 5800 which is widely accepted. According to our calculations, there remain about 200-300 orphans-ORFs without known function or homology to already discovered genes, which is only about 5% of the total number of genes. Our results would be questionable if the analysed set of known genes was not a statistically representative sample of the whole set of protein coding genes in the S. cerevisiae genome. Therefore, we repeated our estimation using recently updated databases. In the course of the last 18 months, previously unknown functions of about 500 genes have been found. We have used these to check our method, former results and conclusions. Our previous estimation of the total number of coding ORFs was confirmed. Copyright (C) 1999 John Wiley & Sons, Ltd.

关键词： coding sequence genome coding capacity open reading frame gene number

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Characterization and subcellular compartmentation of recombinant 4-hydroxyphenylpyruvate dioxygenase from Arabidopsis in transgenic tobacco

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PLANT PHYSIOLOGY 1999年第4期119卷 1507-1516页

作者： Garcia, I Rodgers, M Pepin, R Hsieh, TF Matringe, M Rhone Poulenc CNRS UMR 41 F-69263 Lyon 09 France Rhone Poulenc Agrochim Dept Biotechnol F-69263 Lyon 09 France Texas A&M Univ Dept Biol College Stn TX 77843 USA

4-Hydroxyphenylpyruvate dioxygenase (4HPPD) catalyzes the formation of homogentisate (2,5-dihydroxyphenylacetate) from p-hydroxyphenylpyruvate and molecular oxygen. In plants this enzyme activity is involved in two distinct metabolic processes, the biosynthesis of prenylquinones and the catabolism of tyrosine. We report here the molecular and biochemical characterization of an Arabidopsis 4HPPD and the compartmentation of the recombinant protein in chlorophyllous tissues. We isolated a 1508-bp cDNA with one large open reading frame of 1338 bp. Southern analysis strongly suggested that this Arabidopsis 4HPPD is encoded by a single-copy gene. We investigated the biochemical characteristics of this 4HPPD by overproducing the recombinant protein in Escherichia coli JM105. The subcellular localization of the recombinant 4HPPD in chlorophyllous tissues was examined by overexpressing its complete coding sequence in transgenic tobacco (Nicotiana tabacum), using Agrobacterium tumefaciens transformation. We. performed western analyses for the immunodetection of protein extracts from purified chloroplasts and total leaf extracts and for the immunocytochemistry on tissue sections. These analyses clearly revealed that 4HPPD was confined to the cytosol compartment, not targeted to the chloroplast. Western analyses confirmed the presence of a cytosolic form of 4HPPD in cultured green Arabidopsis cells.

关键词： Recombinant Proteins Arabidopsis Enzymatic activity immunodetection COMPARTMENT 4-hydroxyphenylpyruvate 4-Hydroxyphenylpyruvate Dioxygenase Biochemical characteristics leaf extracts coding sequence Tobacco Products Dioxygen Dioxygenases Subcellular

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The role of components of recombination signal sequences in immunoglobulin gene segment usage: a V81x model

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NUCLEIC ACIDS RESEARCH 1999年第11期27卷 2304-2309页

作者： Larijani, M Yu, CCK Golub, R Lam, QLK Wu, GE Univ Toronto Dept Immunol Toronto ON M5G 2M9 Canada Univ Toronto Ontario Canc Inst Toronto ON M5G 2M9 Canada

It has long been appreciated that some immunoglobulin (and T-cell receptor) gene segments are used much more frequently than others. The V-H Segment V81x is a particularly striking case of overusage, Its usage varies with the stage of B-cell development and with the strain of mice, but it is always high in B cell progenitors. We have found that the coding sequence and the recombination signal sequences (RSS) are identical in five mouse strains, including CAST/Ei, a strain derived from the species Mus castaneus, Thus, the strain differences cannot be attributed to sequences within V81x itself. V81x RSS mediated recombination at rates significantly higher than another V-H RSS, Although the V81x nonamer differs at one base pair from the consensus sequence, an RSS with this nonamer and a consensus heptamer recombines as well as the consensus RSS. When the V81x spacer is replaced by that of VA1, the frequency of recombination decreases by similar to 5-fold;thus, the contribution of variation in natural spacers to variability in V-H usage in vivo is likely to be more than has been previously appreciated, Furthermore, the contribution of the heptamer and nonamer to differential V-H usage in our assay is correlated inversely with their conservation throughout the V-H locus.

关键词： .contribute spacer coding sequence functional analysis RSS recombination signal Gene Segment Nonamer heptamer role of components sequences in immunoglobulin overusage

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Cloning of a mammalian elk potassium channel gene and EAG:: mRNA distribution in rat sympathetic ganglia

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JOURNAL OF PHYSIOLOGY-LONDON 1998年第3期511卷 675-682页

作者： Shi, WM Wang, HS Pan, ZM Wymore, RS Cohen, IS McKinnon, D Dixon, JE SUNY Stony Brook Dept Neurobiol & Behav Stony Brook NY 11794 USA SUNY Stony Brook Dept Physiol & Biophys Stony Brook NY 11794 USA

1. Three new members of the EAG potassium channel gene family were identified in rat and the complete coding sequence of one of these genes (elk1) was determined by cDNA cloning. 2. The elk1 gene, when expressed in Xenopus oocytes, encodes a slowly activating and slowly deactivating potassium channel. 3. The elk1 gene is expressed in sympathetic ganglia and is also expressed in sciatic nerve. 4. Six of the seven known EAG genes were found to be expressed in rat sympathetic ganglia, suggesting an important functional role for these channels in the sympathetic nervous system.

关键词： Ganglia Sympathetic Potassium Channels eag protein elk1-protein DNA Complementary 神经节交感钾通道 Potassium Channels DNA Rats Ganglia sympathetic ganglion Complementary coding sequence Cloning

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The translational signal database, TransTerm, is now a relational database

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NUCLEIC ACIDS RESEARCH 1998年第1期26卷 335-337页

作者： Dalphin, ME Brown, CM Stockwell, PA Tate, WP Univ Otago Dept Biochem Dunedin New Zealand Univ Otago Ctr Gene Res Dunedin New Zealand

TransTerm-97 contains more than 97500 non-redundant coding-sequence initiation and termination contexts compiled from GenBank, release 101 (15-June-1997). In addition, several coding sequence parameters are available: coding sequence length, Nc, GC3, and, when it is computable, codon adaptation index (CAI), Codon usage tables and summaries of start and stop codon contexts are also included, The information covers more than 325 species and organelles, including seven complete bacterial genomes and one complete eukaryotic genome, To promote research in translational control of protein synthesis, TransTerm has been converted into a relational database to ease the process of making queries, The relational database manager, Postgresql, gives access to the database using SQL (Structured Query Language), A World Wide Web interface using forms is being completed to allow the casual user access to the database, Extensions are planned to include the full 5'-UTR, full coding sequence and 3'-UTR, TransTerm-97 is available on the World Wide Web at: http://***:800/Transterm/***.

关键词： Codon Initiator Terminator Databases Factual Translation Genetic 密码子起始终止数据库事实型翻译遗传 Codons Translation Process bacterial genome Relational databases translational control Initiators Terminator Device Component coding sequence SQL Database

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An Integrated sequence-Structure Database incorporating matching mRNA sequence, amino acid sequence and protein three-dimensional structure data

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NUCLEIC ACIDS RESEARCH 1998年第1期26卷 327-331页

作者： Adzhubei, IA Adzhubei, AA Neidle, S Inst Canc Res CRC Biomol Struct Unit Surrey SM2 5NG England Moscow MV Lomonosov State Univ Fac Biol Dept Mol Biol Moscow 119899 Russia

We have constructed a non-homologous database, termed the Integrated sequence-Structure Database (ISSD) which comprises the coding sequences of genes, amino acid sequences of the corresponding proteins, their secondary structure and phi, psi angles assignments, and polypeptide backbone coordinates, Each protein entry in the database holds the alignment of nucleotide sequence, amino acid sequence and the PDB three-dimensional structure data, The nucleotide and amino acid sequences for each entry are selected on the basis of exact matches of the source organism and cell environment, The current version 1.0 of ISSD is available on the WWW at http://***/issd/ and includes 107 non-homologous mammalian proteins, of which 80 are human proteins, The database has been used by us for the analysis of synonymous codon usage patterns in mRNA sequences showing their correlation with the three-dimensional structure features in the encoded proteins, Possible ISSD applications include optimisation of protein expression, improvement of the protein structure prediction accuracy, and analysis of evolutionary aspects of the nucleotide sequence-protein structure relationship.

关键词： Databases Factual Nucleic Acid Conformation Protein Conformation RNA Messenger 数据库事实型核酸构象蛋白质构象信使 Nucleic Acid Conformation Amino Acid sequence messengers NR4A2 protein, human Protein Conformation RNA coding sequence Database Nucleotides

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THE coding sequence OF THE BOVINE FERROCHELATASE GENE

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BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1995年第1期1231卷 117-120页

作者： SHIBUYA, H NONNEMAN, D TAMASSIA, M ALLPHIN, OL JOHNSON, GS UNIV MISSOURI DEPT VET MED & SURGCOLUMBIAMO 65211

The amino acid code and surrounding regions in the bovine ferrochelatase gene were amplified by a combination of reverse transcriptase PCR and vectorette PCR and sequenced. The bovine code was 86% homologous to the hu... 详细信息

关键词： FERROCHELATASE GENE VECTORETTE PCR coding sequence PCR (BOVINE)

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REDEFINITION OF THE coding sequence OF THE MXI1 GENE AND IDENTIFICATION OF A POLYMORPHIC REPEAT IN THE 3' NONcoding REGION THAT ALLOWS THE DETECTION OF LOSS OF HETEROZYGOSITY OF CHROMOSOME 10Q25 IN GLIOBLASTOMAS

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HUMAN GENETICS 1995年第6期95卷 709-711页

作者： ALBAROSA, R DIDONATO, S FINOCCHIARO, G IST NAZL NEUROL C BESTA DIV BIOCHIM & GENETI-20133 MILANITALY

The MXI1 gene encodes a protein interacting with Max, a regulatory factor of the Myc oncogene, and is located on chromosome 10q25, a region showing frequent loss of heterozygosity in malignant gliomas. We have reassessed the coding sequence of MXI1 and found that, at the 3' end, the open reading frame is 28 codons shorter than previously described. We have also found an AAAAC polymorphic repeat (two alleles, 45% heterozygosity) in the 3' non-coding region of the gene. Six anaplastic astrocytomas and nine glioblastomas, the most malignant form of glioma, were informative for this polymorphism. Loss of heterozygosity was demonstrated in all glioblastomas, but not in the remaining tumors.

关键词： Malignant Glioma Chromosomes Lipoblastoma redefinition coding sequence Loss of Heterozygosity oncogene myc 10q25 heterozygosity

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