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Pesquisa : G05.360.340.024.340.385.600 [Categoria DeCS]
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  1 / 25 MEDLINE  
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[PMID]:25666524
[Au] Autor:Yan T; Zhu JR; Di D; Gao Q; Zhang Y; Zhang A; Yan C; Miao H; Wang XB
[Ad] Endereço:State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China. Electronic address: yantengforever@gmail.com.
[Ti] Título:Characterization of the complete genome of Barley yellow striate mosaic virus reveals a nested gene encoding a small hydrophobic protein.
[So] Source:Virology;478:112-22, 2015 Apr.
[Is] ISSN:1096-0341
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Barley yellow striate mosaic virus (BYSMV), a member of the genus Cytorhabdovirus, causes serious crop losses in agriculture. Here, we have cloned the BYSMV-derived small interfering RNAs (siRNAs), assembled the siRNAs and used RT-PCR to reconstruct the BYSMV genome. The genome consists of 12,706 nucleotides and encodes ten predicted genes from the antigenomic strand. The major BYSMV structural proteins share identities ranging from 35% to 62% with northern cereal mosaic virus (NCMV) counterparts. A notable difference is that BYSMV contains three transcriptional units residing between the P and M genes compared with four units in the corresponding region of NCMV. Unexpectedly, the middle mRNA in this region encodes gene5 nested in an alternative frame within gene4 via a leaky scanning mechanism. The gene5 encodes a small hydrophobic protein targeting to the endoplasmic reticulum (ER). To our knowledge, this is the first report of nested gene in plant rhabdoviruses.
[Mh] Termos MeSH primário: Genoma Viral
Interações Hidrofóbicas e Hidrofílicas
Genes Inseridos
RNA Viral/genética
Rhabdoviridae/genética
Proteínas Virais/química
Proteínas Virais/genética
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Sequência de Bases
Genes Virais
Hordeum/virologia
Dados de Sequência Molecular
Rhabdoviridae/isolamento & purificação
Análise de Sequência de DNA
Homologia de Sequência de Aminoácidos
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (RNA, Viral); 0 (Viral Proteins)
[Em] Mês de entrada:1506
[Cu] Atualização por classe:150316
[Lr] Data última revisão:
150316
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150211
[St] Status:MEDLINE


  2 / 25 MEDLINE  
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[PMID]:25571900
[Au] Autor:Mathews EA; Mullen GP; Manjarrez JR; Rand JB
[Ad] Endereço:Genetic Models of Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104.
[Ti] Título:Unusual regulation of splicing of the cholinergic locus in Caenorhabditis elegans.
[So] Source:Genetics;199(3):729-37, 2015 Mar.
[Is] ISSN:1943-2631
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The essential neurotransmitter acetylcholine functions throughout the animal kingdom. In Caenorhabditis elegans, the acetylcholine biosynthetic enzyme [choline acetyltransferase (ChAT)] and vesicular transporter [vesicular acetylcholine transporter (VAChT)] are encoded by the cha-1 and unc-17 genes, respectively. These two genes compose a single complex locus in which the unc-17 gene is nested within the first intron of cha-1, and the two gene products arise from a common pre-messenger RNA (pre-mRNA) by alternative splicing. This genomic organization, known as the cholinergic gene locus (CGL), is conserved throughout the animal kingdom, suggesting that the structure is important for the regulation and function of these genes. However, very little is known about CGL regulation in any species. We now report the identification of an unusual type of splicing regulation in the CGL of C. elegans, mediated by two pairs of complementary sequence elements within the locus. We show that both pairs of elements are required for efficient splicing to the distal acceptor, and we also demonstrate that proper distal splicing depends more on sequence complementarity within each pair of elements than on the sequences themselves. We propose that these sequence elements are able to form stem-loop structures in the pre-mRNA; such structures would favor specific splicing alternatives and thus regulate CGL splicing. We have identified complementary elements at comparable locations in the genomes of representative species of other animal phyla; we suggest that this unusual regulatory mechanism may be a general feature of CGLs.
[Mh] Termos MeSH primário: Proteínas de Caenorhabditis elegans/genética
Caenorhabditis elegans/genética
Colina O-Acetiltransferase/genética
Genes Inseridos
Processamento de RNA
Proteínas Vesiculares de Transporte de Acetilcolina/genética
[Mh] Termos MeSH secundário: Animais
Evolução Molecular
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Caenorhabditis elegans Proteins); 0 (Unc-17 protein, C elegans); 0 (Vesicular Acetylcholine Transport Proteins); EC 2.3.1.6 (Choline O-Acetyltransferase)
[Em] Mês de entrada:1511
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150110
[St] Status:MEDLINE
[do] DOI:10.1534/genetics.114.173765


  3 / 25 MEDLINE  
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[PMID]:24084778
[Au] Autor:Lee YC; Chang HH
[Ad] Endereço:Center for Population Biology and Department of Evolution and Ecology, University of California.
[Ti] Título:The evolution and functional significance of nested gene structures in Drosophila melanogaster.
[So] Source:Genome Biol Evol;5(10):1978-85, 2013.
[Is] ISSN:1759-6653
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Nearly 10% of the genes in the genome of Drosophila melanogaster are in nested structures, in which one gene is completely nested within the intron of another gene (nested and including gene, respectively). Even though the coding sequences and untranslated regions of these nested/including gene pairs do not overlap, their intimate structures and the possibility of shared regulatory sequences raise questions about the evolutionary forces governing the origination and subsequent functional and evolutionary impacts of these structures. In this study, we show that nested genes experience weaker evolutionary constraint, have faster rates of protein evolution, and are expressed in fewer tissues than other genes, while including genes show the opposite patterns. Surprisingly, despite completely overlapping with each other, nested and including genes are less likely to display correlated gene expression and biological function than the nearby yet nonoverlapping genes. Interestingly, significantly fewer nested genes are transcribed from the same strand as the including gene. We found that same-strand nested genes are more likely to be single-exon genes. In addition, same-strand including genes are less likely to have known lethal or sterile phenotypes than opposite-strand including genes only when the corresponding nested genes have introns. These results support our hypothesis that selection against potential erroneous mRNA splicing when nested and including genes are on the same strand plays an important role in the evolution of nested gene structures.
[Mh] Termos MeSH primário: Evolução Molecular
Íntrons/genética
Genes Inseridos
Regiões não Traduzidas/genética
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Animais
Drosophila melanogaster/genética
Éxons/genética
Fenótipo
Processamento de RNA/genética
Transcrição Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Untranslated Regions)
[Em] Mês de entrada:1405
[Cu] Atualização por classe:150422
[Lr] Data última revisão:
150422
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:131003
[St] Status:MEDLINE
[do] DOI:10.1093/gbe/evt149


  4 / 25 MEDLINE  
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[PMID]:22022525
[Au] Autor:Kaer K; Branovets J; Hallikma A; Nigumann P; Speek M
[Ad] Endereço:Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia.
[Ti] Título:Intronic L1 retrotransposons and nested genes cause transcriptional interference by inducing intron retention, exonization and cryptic polyadenylation.
[So] Source:PLoS One;6(10):e26099, 2011.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Transcriptional interference has been recently recognized as an unexpectedly complex and mostly negative regulation of genes. Despite a relatively few studies that emerged in recent years, it has been demonstrated that a readthrough transcription derived from one gene can influence the transcription of another overlapping or nested gene. However, the molecular effects resulting from this interaction are largely unknown. METHODOLOGY/PRINCIPAL FINDINGS: Using in silico chromosome walking, we searched for prematurely terminated transcripts bearing signatures of intron retention or exonization of intronic sequence at their 3' ends upstream to human L1 retrotransposons, protein-coding and noncoding nested genes. We demonstrate that transcriptional interference induced by intronic L1s (or other repeated DNAs) and nested genes could be characterized by intron retention, forced exonization and cryptic polyadenylation. These molecular effects were revealed from the analysis of endogenous transcripts derived from different cell lines and tissues and confirmed by the expression of three minigenes in cell culture. While intron retention and exonization were comparably observed in introns upstream to L1s, forced exonization was preferentially detected in nested genes. Transcriptional interference induced by L1 or nested genes was dependent on the presence or absence of cryptic splice sites, affected the inclusion or exclusion of the upstream exon and the use of cryptic polyadenylation signals. CONCLUSIONS/SIGNIFICANCE: Our results suggest that transcriptional interference induced by intronic L1s and nested genes could influence the transcription of the large number of genes in normal as well as in tumor tissues. Therefore, this type of interference could have a major impact on the regulation of the host gene expression.
[Mh] Termos MeSH primário: Éxons/genética
Íntrons/genética
Genes Inseridos/genética
Poliadenilação/genética
Retroelementos/genética
Transcrição Genética
[Mh] Termos MeSH secundário: Transportadores de Cassetes de Ligação de ATP/genética
Sequência de Bases
Etiquetas de Sequências Expressas
Células HeLa
Seres Humanos
Internet
Modelos Biológicos
Fases de Leitura Aberta/genética
Especificidade de Órgãos/genética
Sítios de Splice de RNA/genética
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
Vírus 40 dos Símios/genética
Transfecção
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (RNA Splice Sites); 0 (RNA, Messenger); 0 (Retroelements)
[Em] Mês de entrada:1202
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:111025
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0026099


  5 / 25 MEDLINE  
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[PMID]:21598020
[Au] Autor:Smith JD; Meehan MH; Crean J; McCann A
[Ad] Endereço:UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin (UCD), Belfield, Dublin 4, Ireland.
[Ti] Título:Alpha T-catenin (CTNNA3): a gene in the hand is worth two in the nest.
[So] Source:Cell Mol Life Sci;68(15):2493-8, 2011 Aug.
[Is] ISSN:1420-9071
[Cp] País de publicação:Switzerland
[La] Idioma:eng
[Ab] Resumo:Alpha-T-Catenin (CTNNA3) is a key protein of the adherens junctional complex in epithelial cells playing a crucial role in cellular adherence. What makes this gene particularly interesting is that it is located within a common fragile site, is epigenetically regulated, is transcribed through multiple promoters, and generates a variety of alternate transcripts. Finally, CTNNA3 has a nested gene (LRTMM3) embedded within its genomic context transcribed in the opposite direction. Apart from the complexity of its regulation, alterations in both CTNNA3 and LRTMM3 are implicated in human disease.
[Mh] Termos MeSH primário: Genes Inseridos/genética
alfa Catenina/genética
alfa Catenina/fisiologia
[Mh] Termos MeSH secundário: Doença de Alzheimer/genética
Animais
Adesão Celular/genética
Epigênese Genética/fisiologia
Regulação da Expressão Gênica
Seres Humanos
Proteínas de Membrana/genética
Proteínas do Tecido Nervoso/genética
Genes Inseridos/fisiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (CTNNA3 protein, human); 0 (LRRTM3 protein, human); 0 (Membrane Proteins); 0 (Nerve Tissue Proteins); 0 (alpha Catenin)
[Em] Mês de entrada:1109
[Cu] Atualização por classe:170915
[Lr] Data última revisão:
170915
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:110521
[St] Status:MEDLINE
[do] DOI:10.1007/s00018-011-0728-0


  6 / 25 MEDLINE  
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[PMID]:20870612
[Au] Autor:Tuju CL; Lü GT; Zeng CQ
[Ad] Endereço:Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 100029, China. tujchl02@163.com
[Ti] Título:[Systematic analysis of cis-nested gene pairs in the human genome].
[So] Source:Yi Chuan;32(9):914-20, 2010 Sep.
[Is] ISSN:0253-9772
[Cp] País de publicação:China
[La] Idioma:chi
[Ab] Resumo:In the genome one gene, whose entire or the most part of the sequence localizes in an intronic or UTR region of another larger gene, is called nested gene. A nested gene pair consists of a host and a nested gene. Here, we conducted a systematic scanning and analysis to identify all cis-nested gene pairs and their structural features in the human genome. Meanwhile, we also explored possible mechanism for evolution of nested gene and the relationship between the host and the cis-nested gene (denoted as nested gene in short). Our analysis indicated that evolution of nested gene pair probably arose from the transposition, de novo mutation, and the mutations occurred in transcription start or termination sites. The change in transcription starting or ending site could be a unique mechanism driving evolution of nested gene pair. Gene Ontology analysis indicated the gene products of the nested gene and its host counterpart have no functional correlation.
[Mh] Termos MeSH primário: Genoma Humano/genética
Íntrons/genética
Genes Inseridos/fisiologia
Transcrição Genética/fisiologia
[Mh] Termos MeSH secundário: Sequência de Bases
Evolução Molecular
Genoma Humano/fisiologia
Seres Humanos
Íntrons/fisiologia
Genes Inseridos/genética
[Pt] Tipo de publicação:ENGLISH ABSTRACT; JOURNAL ARTICLE
[Em] Mês de entrada:1011
[Cu] Atualização por classe:161020
[Lr] Data última revisão:
161020
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:100928
[St] Status:MEDLINE


  7 / 25 MEDLINE  
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[PMID]:20516662
[Au] Autor:Chester M; Sykorova E; Fajkus J; Leitch AR
[Ad] Endereço:School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
[Ti] Título:Single integration and spread of a Copia-like sequence nested in rDNA intergenic spacers of Allium cernuum (Alliaceae).
[So] Source:Cytogenet Genome Res;129(1-3):35-46, 2010 Jul.
[Is] ISSN:1424-859X
[Cp] País de publicação:Switzerland
[La] Idioma:eng
[Ab] Resumo:The 35S ribosomal DNA (rDNA) intergenic spacer (IGS) of Allium cernuum is examined. Initial sequencing of IGS clones revealed that some rDNA units contain a truncated retrotransposon sequence most similar to members of the Copia superfamily. Fluorescence in situ hybridisation (FISH) to metaphase chromosomes indicates that this element is dispersed along both pairs of major rDNA arrays. Southern hybridisation confirmed the presence of this 'relic' Copia-like element in more than 10% of 35S rDNA units, in the same position within the IGS. To measure the intragenomic divergence of the relic retroelement and its flanking sequences amongst different rDNA units, a 1.1-kb region was amplified and cloned. These data collectively point to a single origin for units containing the putative retrotransposon fragment. It is likely that units containing the putative retroelement increased in copy number and dispersed via rDNA homogenisation mechanisms, rather than by multiple retrotransposition events.
[Mh] Termos MeSH primário: Allium/genética
DNA de Plantas/genética
DNA Espaçador Ribossômico/genética
Retroelementos/genética
[Mh] Termos MeSH secundário: Allium/classificação
Sequência de Bases
Southern Blotting
Cromossomos de Plantas/genética
Primers do DNA/genética
Evolução Molecular
Variação Genética
Genoma de Planta
Hibridização in Situ Fluorescente
Genes Inseridos
Filogenia
Especificidade da Espécie
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA Primers); 0 (DNA, Plant); 0 (DNA, Ribosomal Spacer); 0 (Retroelements)
[Em] Mês de entrada:1008
[Cu] Atualização por classe:100714
[Lr] Data última revisão:
100714
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:100603
[St] Status:MEDLINE
[do] DOI:10.1159/000312959


  8 / 25 MEDLINE  
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[PMID]:19542305
[Au] Autor:Kumar A
[Ad] Endereço:Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-2216, USA. anujk@umich.edu
[Ti] Título:An overview of nested genes in eukaryotic genomes.
[So] Source:Eukaryot Cell;8(9):1321-9, 2009 Sep.
[Is] ISSN:1535-9786
[Cp] País de publicação:United States
[La] Idioma:eng
[Mh] Termos MeSH primário: Células Eucarióticas/metabolismo
Genoma
Genes Inseridos
[Mh] Termos MeSH secundário: Animais
Evolução Molecular
Regulação da Expressão Gênica
Seres Humanos
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.; REVIEW
[Em] Mês de entrada:0912
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:090623
[St] Status:MEDLINE
[do] DOI:10.1128/EC.00143-09


  9 / 25 MEDLINE  
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[PMID]:19286988
[Au] Autor:Zweifel E; Smith J; Romero D; Giddings TH; Winey M; Honts J; Dahlseid J; Schneider B; Cole ES
[Ad] Endereço:Biology Department, St. Olaf College, 1520 St. Olaf Ave., Northfield, MN 55057, USA.
[Ti] Título:Nested genes CDA12 and CDA13 encode proteins associated with membrane trafficking in the ciliate Tetrahymena thermophila.
[So] Source:Eukaryot Cell;8(6):899-912, 2009 Jun.
[Is] ISSN:1535-9786
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:We describe a novel pair of nested genes, CDA12 and CDA13, from Tetrahymena thermophila. Both are implicated in membrane trafficking associated with cell division and conjugation. Green fluorescent protein localization reveals Cda12p decoration of diverse membrane-bound compartments, including mobile, subcortical tubulovesicular compartments; perinuclear vesicles; and candidates for recycling endosomes. Cda13p decorates intracellular foci located adjacent to cortically aligned mitochondria and their neighboring Golgi networks. The expression of antisense CDA12 RNA in transformants produces defects in cytokinesis, macronuclear segregation, and the processing of pinosomes to downstream compartments. Antisense CDA13 RNA expression produces a conjugation phenotype, resulting in the failure of mating pairs to separate, as well as failures in postconjugation cytokinesis and macronuclear fission. This study offers insight into the membrane trafficking events linking endosome and Golgi network activities, cytokinesis, and karyokinesis and the unique membrane-remodeling events that accompany conjugation in the ciliate T. thermophila. We also highlight an unusual aspect of genome organization in Tetrahymena, namely, the existence of nested, antisense genes.
[Mh] Termos MeSH primário: Membrana Celular/metabolismo
Genes Inseridos
Proteínas de Protozoários/genética
Proteínas de Protozoários/metabolismo
Tetrahymena thermophila/genética
Tetrahymena thermophila/metabolismo
[Mh] Termos MeSH secundário: Animais
Membrana Celular/genética
Citocinese
Dados de Sequência Molecular
Transporte Proteico
Tetrahymena thermophila/citologia
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (Protozoan Proteins)
[Em] Mês de entrada:0908
[Cu] Atualização por classe:170220
[Lr] Data última revisão:
170220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:090317
[St] Status:MEDLINE
[do] DOI:10.1128/EC.00342-08


  10 / 25 MEDLINE  
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[PMID]:19052635
[Au] Autor:Wang X; Sun Q; McGrath SD; Mardis ER; Soloway PD; Clark AG
[Ad] Endereço:Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA.
[Ti] Título:Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain.
[So] Source:PLoS One;3(12):e3839, 2008.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Imprinted genes display differential allelic expression in a manner that depends on the sex of the transmitting parent. The degree of imprinting is often tissue-specific and/or developmental stage-specific, and may be altered in some diseases including cancer. Here we applied Illumina/Solexa sequencing of the transcriptomes of reciprocal F1 mouse neonatal brains and identified 26 genes with parent-of-origin dependent differential allelic expression. Allele-specific Pyrosequencing verified 17 of them, including three novel imprinted genes. The known and novel imprinted genes all are found in proximity to previously reported differentially methylated regions (DMRs). Ten genes known to be imprinted in placenta had sufficient expression levels to attain a read depth that provided statistical power to detect imprinting, and yet all were consistent with non-imprinting in our transcript count data for neonatal brain. Three closely linked and reciprocally imprinted gene pairs were also discovered, and their pattern of expression suggests transcriptional interference. Despite the coverage of more than 5000 genes, this scan only identified three novel imprinted refseq genes in neonatal brain, suggesting that this tissue is nearly exhaustively characterized. This approach has the potential to yield an complete catalog of imprinted genes after application to multiple tissues and developmental stages, shedding light on the mechanism, bioinformatic prediction, and evolution of imprinted genes and diseases associated with genomic imprinting.
[Mh] Termos MeSH primário: Encéfalo/metabolismo
Regulação da Expressão Gênica no Desenvolvimento
Impressão Genômica/genética
[Mh] Termos MeSH secundário: Alelos
Animais
Animais Recém-Nascidos
Encéfalo/crescimento & desenvolvimento
Perfilação da Expressão Gênica
Camundongos
Camundongos Endogâmicos AKR
Camundongos Endogâmicos C3H
Camundongos Endogâmicos C57BL
Genes Inseridos
Polimorfismo de Nucleotídeo Único
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:0902
[Cu] Atualização por classe:140901
[Lr] Data última revisão:
140901
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:081205
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0003839



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