Database and analyses of known alternatively spliced genes in plants.

Abstract:

:Alternative splicing is an important cellular mechanism that increases the diversity of gene products. The number of alternatively spliced genes reported so far in plants is much smaller than that in mammals, but is increasing as a result of the explosive growth of available EST and genomic sequences. We have searched for all alternatively spliced genes reported in GenBank and PubMed in all plant species under Viridiplantae. After careful merging and manual review of the search results, we obtained a comprehensive, high-quality collection of 168 genes reported to be alternatively spliced in plants, spanning 44 plant species (March 22, 2003 update). We developed a relational database with Web-based user interface to store and present the data, named the Plant Alternative Splicing Database (PASDB), freely available at http://pasdb.genomics.org.cn. We analyzed the functional categories that these genes belong to using the Gene Ontology. We also analyzed in detail the biological roles and gene structures of the four genes that are known to be alternatively spliced in more than one plant species. Finally, we studied the structural features of the splice sites in the alternatively spliced genes.

journal_name

Genomics

journal_title

Genomics

authors

Zhou Y,Zhou C,Ye L,Dong J,Xu H,Cai L,Zhang L,Wei L

doi

10.1016/s0888-7543(03)00204-0

subject

Has Abstract

pub_date

2003-12-01 00:00:00

pages

584-95

issue

6

eissn

0888-7543

issn

1089-8646

pii

S0888754303002040

journal_volume

82

pub_type

杂志文章

相关文献

GENOMICS文献大全
  • Zinc finger protein gene complexes on mouse chromosomes 8 and 11.

    abstract::Two murine homologs of the Drosophila Krüppel gene, a member of the gap class of developmental control genes that encode a protein with zinc fingers, were mapped to mouse chromosomes 8 and 11 by using somatic cell hybrids and an interspecific backcross. Surprisingly, both genes were closely linked to two previously ma...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(90)90033-q

    authors: Nadeau JH,Birkenmeier CS,Chowdhury K,Crosby JL,Lalley PA

    更新日期:1990-11-01 00:00:00

  • Isolation and chromosomal localization of a novel FMS-like tyrosine kinase gene.

    abstract::We have isolated and sequenced part of a new gene of the tyrosine kinase family. This gene, called FLT3, has strong sequence similarities with members of a group of genes encoding growth factor receptors: FMS, KIT, and PDGFR. We have localized the human FLT3 gene to chromosome 13, band q12, and its mouse homolog to ch...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(91)90270-o

    authors: Rosnet O,Matteï MG,Marchetto S,Birnbaum D

    更新日期:1991-02-01 00:00:00

  • Assignment of xeroderma pigmentosum group C (XPC) gene to chromosome 3p25.

    abstract::The human gene XPC (formerly designated XPCC), which corrects the repair deficiency of xeroderma pigmentosum (XP) group C cells, was mapped to 3p25. A cDNA probe for Southern blot hybridization and diagnostic PCR analyses of hybrid clone panels informative for human chromosomes in general and portions of chromosome 3 ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1994.1256

    authors: Legerski RJ,Liu P,Li L,Peterson CA,Zhao Y,Leach RJ,Naylor SL,Siciliano MJ

    更新日期:1994-05-01 00:00:00

  • Fine-scale comparative mapping of the human 7q11.23 region and the orthologous region on mouse chromosome 5G: the low-copy repeats that flank the Williams-Beuren syndrome deletion arose at breakpoint sites of an evolutionary inversion(s).

    abstract::Williams-Beuren syndrome (WBS) is a developmental disorder caused by haploinsufficiency for genes deleted in chromosome band 7q11.23. A common deletion including at least 16-17 genes has been defined in the great majority of patients. We have completed a physical and transcription map of the WBS region based on analys...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.2000.6312

    authors: Valero MC,de Luis O,Cruces J,Pérez Jurado LA

    更新日期:2000-10-01 00:00:00

  • Localization of eight additional genes in the human major histocompatibility complex, including the gene encoding the casein kinase II beta subunit (CSNK2B).

    abstract::A wide range of autoimmune and other diseases are known to be associated with the major histocompatibility complex. Many of these diseases are linked to the genes encoding the polymorphic histocompatibility antigens in the class I and class II regions, but some appear to be more strongly associated with genes in the c...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1996.0459

    authors: Albertella MR,Jones H,Thomson W,Olavesen MG,Campbell RD

    更新日期:1996-09-01 00:00:00

  • A high-resolution genetic map of the nervous locus on mouse chromosome 8.

    abstract::The nervous (nr) mutant mouse displays two gross recessive traits: both an exaggeration of juvenile hyperactivity and a pronounced ataxia become apparent during the third and fourth postnatal weeks. Using an intersubspecific intercross, we have established a high-resolution map of a segment of mouse chromosome 8 that ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1997.5193

    authors: De Jager PL,Harvey D,Polydorides AD,Zuo J,Heintz N

    更新日期:1998-03-15 00:00:00

  • Fibulin-2 (FBLN2): human cDNA sequence, mRNA expression, and mapping of the gene on human and mouse chromosomes.

    abstract::Fibulin-2 is a new extracellular matrix protein that we recently identified by characterizing mouse cDNA clones. Fibulin-2 mRNA is prominently expressed in mouse heart tissue and is present in low amounts in other tissues. In this study, we isolated and sequenced a 4.1-kb human fibulin-2 cDNA, which encoded a mature p...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1994.1404

    authors: Zhang RZ,Pan TC,Zhang ZY,Mattei MG,Timpl R,Chu ML

    更新日期:1994-07-15 00:00:00

  • Structure, chromosomal location, and expression pattern of three mouse genes homologous to the human MAGE genes.

    abstract::The human MAGE1 gene directs the expression of an antigen recognized on a melanoma by autologous cytolytic T lymphocytes. MAGE1 belongs to a family of genes that are expressed in a number of tumors of various histological types but not in normal tissues except testis. The MAGE genes are arranged in two groups that are...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1995.1108

    authors: De Backer O,Verheyden AM,Martin B,Godelaine D,De Plaen E,Brasseur R,Avner P,Boon T

    更新日期:1995-07-01 00:00:00

  • Pseudomonas putida modulates the expression of miRNAs and their target genes in response to drought and salt stresses in chickpea (Cicer arietinum L.).

    abstract::MicroRNAs are small non-coding regulatory RNA molecules that play an important role in the modulation of gene expression during various environmental stresses. Pseudomonas putida RA, a plant growth promoting rhizobacteria (PGPR) colonizes the root surface of plants improving their growth and development during abiotic...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2018.01.007

    authors: Jatan R,Chauhan PS,Lata C

    更新日期:2019-07-01 00:00:00

  • The complete sequences of the galago and rabbit beta-globin locus control regions: extended sequence and functional conservation outside the cores of DNase hypersensitive sites.

    abstract::The locus control region (LCR) of mammalian beta-globin genes covers at least 17 kb at the 5' end of the gene cluster and has been implicated in chromatin domain opening, enhancement, and insulation from neighboring sequences. Functional dissection of the LCR has defined the minimal cores for four of the five major DN...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1996.4458

    authors: Slightom JL,Bock JH,Tagle DA,Gumucio DL,Goodman M,Stojanovic N,Jackson J,Miller W,Hardison R

    更新日期:1997-01-01 00:00:00

  • Exon-intron structure of a 2.7-kb transcript of the STM7 gene with phosphatidylinositol-4-phosphate 5-kinase activity.

    abstract::The STM7 gene encodes a novel phosphatidylinositol-4-phosphate 5-kinase (PtdInsP 5-kinase) that is subject to alternative splicing and developmental control. We have recently presented data indicating that several splice variants of STM7 incorporate elements of the X25 sequence, previously implicated in the pathogenes...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1997.4726

    authors: Pook MA,Carvajal JJ,Doudney K,Hillermann R,Chamberlain S

    更新日期:1997-05-15 00:00:00

  • Characterization of the genomic structure of the mouse APLP1 gene.

    abstract::Amyloid beta protein (beta A4), the major component of the core of amyloid plaques in Alzheimer disease, is derived from the transmembrane amyloid precursor proteins (APPs). Our recent studies showed that a murine member of the evolutionarily conserved APP family, amyloid precursor-like protein 1 (APLP1), is specifica...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1996.0096

    authors: Zhong S,Wu K,Black IB,Schaar DG

    更新日期:1996-02-15 00:00:00

  • MiR-373 exacerbates renal injury and fibrosis via NF-κB/MatrixMetalloproteinase-9 signaling by targeting Sirtuin1.

    abstract:BACKGROUND:Renal fibrosis is a final common pathway of chronic kidney disease. SIRT1, a NAD+-dependent protein deacetylase, deacetylates the p65 of NF-κB and shows protective effects in kidney disorders. miR-373 directly targets the 3'UTR of SIRT1. However, roles of miR-373 in renal fibrosis are unclear. METHODS:TGF-β...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2018.04.017

    authors: Yang H,Liao D,Tong L,Zhong L,Wu K

    更新日期:2019-07-01 00:00:00

  • Ontological Discovery Environment: a system for integrating gene-phenotype associations.

    abstract::The wealth of genomic technologies has enabled biologists to rapidly ascribe phenotypic characters to biological substrates. Central to effective biological investigation is the operational definition of the process under investigation. We propose an elucidation of categories of biological characters, including diseas...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2009.08.016

    authors: Baker EJ,Jay JJ,Philip VM,Zhang Y,Li Z,Kirova R,Langston MA,Chesler EJ

    更新日期:2009-12-01 00:00:00

  • Major rearrangements in the alpha 5(IV) collagen gene in three patients with Alport syndrome.

    abstract::The gene coding for the alpha 5 chian of type IV collagen (alpha 5(IV) collagen), which maps to Xq22, is a candidate gene for the X-linked dominant disease Alport syndrome (AS). Using three cDNA clones, covering the 3' end of the alpha 5(IV) collagen gene, 3 of 38 patients have been identified with mutations in this g...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(91)90040-l

    authors: Boye E,Vetrie D,Flinter F,Buckle B,Pihlajaniemi T,Hamalainen ER,Myers JC,Bobrow M,Harris A

    更新日期:1991-12-01 00:00:00

  • A yeast artificial chromosome contig of the critical region for cri-du-chat syndrome.

    abstract::Cri-du-chat is a chromosomal deletion syndrome characterized by partial deletion of the short arm of chromosome 5. The clinical symptoms include growth and mental retardation, microcephaly, hypertelorism, epicanthal folds, hypotonia, and a high-pitched monochromatic cry that is usually considered diagnostic for the sy...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1994.1582

    authors: Goodart SA,Simmons AD,Grady D,Rojas K,Moyzis RK,Lovett M,Overhauser J

    更新日期:1994-11-01 00:00:00

  • Neurturin, a novel neurotrophic factor, is localized to mouse chromosome 17 and human chromosome 19p13.3.

    abstract::Neurturin is a potent neurotrophic factor closely related to glial cell line-derived neurotrophic factor (GDNF, 40% amino acid sequence identity) and, like GDNF, can promote the survival of numerous neuronal populations including sympathetic, nodose, and dorsal root ganglion sensory neurons. Both neurturin and GDNF si...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1997.4846

    authors: Heuckeroth RO,Kotzbauer P,Copeland NG,Gilbert DJ,Jenkins NA,Zimonjic DB,Popescu NC,Johnson EM Jr,Milbrandt J

    更新日期:1997-08-15 00:00:00

  • Molecular cloning and characterization of a novel mouse epidermal differentiation gene and its promoter.

    abstract::The transcription factor E2F1 is an important regulator of cell proliferation, apoptosis, and differentiation. A novel mouse gene (Eig3) was originally identified as up-regulated in E2F1-overexpressing keratinocytes by the rapid analysis of gene expression technique. An apparently full-length cDNA and a 2.8-kb genomic...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.2001.6518

    authors: Wang A,Johnson DG,MacLeod MC

    更新日期:2001-05-01 00:00:00

  • A large duplicated area in the polycystic kidney disease 1 (PKD1) region of chromosome 16 is prone to rearrangement.

    abstract::An area of 500 kb at the proximal end of the polycystic kidney disease 1 (PKD1) region has been mapped in detail, with 260 kb cloned in cosmids. The area cloned from normal individuals contains two homologous but divergent regions each of 75 kb, including the previously described marker 26-6. Pulsed-field gel electrop...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1994.1507

    authors: Harris PC,Thomas S,MacCarthy AB,Stallings RL,Breuning MH,Jenne DE,Fink TM,Buckle VJ,Ratcliffe PJ,Ward CJ

    更新日期:1994-09-15 00:00:00

  • Structure and polymorphism of the mouse myelin/oligodendrocyte glycoprotein gene.

    abstract::We have isolated and characterized genomic clones containing the mouse myelin/oligodendrocyte glycoprotein (MOG) gene. It spans a region of 12.5 kb and consists of eight exons. Its exon-intron structure differs from that of classical MHC-class I genes, with which it is linked in the mouse genome. Nucleotide sequencing...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1994.1456

    authors: Daubas P,Pham-Dinh D,Dautigny A

    更新日期:1994-09-01 00:00:00

  • A new dominant retinal degeneration (Rd4) associated with a chromosomal inversion in the mouse.

    abstract::An autosomal dominant retinal degeneration, called Rd4, was found in a stock carrying the inversion In(4)56Rk, which was induced in a DBA/2J male. The inversion encompasses nearly all of Chromosome 4. It is homozygous lethal and in heterozygotes is always associated with retinal degeneration. In affected mice, the ret...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1997.4717

    authors: Roderick TH,Chang B,Hawes NL,Heckenlively JR

    更新日期:1997-06-15 00:00:00

  • Genomic definition of RIM proteins: evolutionary amplification of a family of synaptic regulatory proteins.

    abstract::RIMs are synaptic proteins that are essential for normal neurotransmitter release. We now show that while invertebrates contain only a single RIM gene, vertebrates contain four: two large genes encoding RIM1alpha (0.50 Mb) or RIM2alpha, 2beta, and 2gamma (0.50-0.75 Mb) and two smaller genes encoding RIM3gamma (14 kb) ...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/s0888-7543(02)00024-1

    authors: Wang Y,Südhof TC

    更新日期:2003-02-01 00:00:00

  • Genome analysis provides insights into crude oil degradation and biosurfactant production by extremely halotolerant Halomonas desertis G11 isolated from Chott El-Djerid salt-lake in Tunisian desert.

    abstract::Here, we report the genomic features and the bioremediation potential of Halomonas desertis G11, a new halophilic species which uses crude oil as a carbon and energy source and displays intrinsic resistance to salt stress conditions (optimum growth at 10% NaCl). G11 genome (3.96 Mb) had a mean GC content of 57.82%, 36...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2018.12.003

    authors: Neifar M,Chouchane H,Najjari A,El Hidri D,Mahjoubi M,Ghedira K,Naili F,Soufi L,Raddadi N,Sghaier H,Ouzari HI,Masmoudi AS,Cherif A

    更新日期:2019-12-01 00:00:00

  • Relationship of the genes for Chediak-Higashi syndrome (beige) and the T-cell receptor gamma chain in mouse and man.

    abstract::The genetic linkage of Chediak-Higashi syndrome and its murine analog, beige (bg), to the T-cell receptor (TCR-gamma) gamma chain gene is further defined. Previous studies using recombinant inbred strains of mice demonstrated that the murine bg gene is genetically linked to a murine TCR-gamma gene. We report that in t...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(87)90058-9

    authors: Holcombe RF,Strauss W,Owen FL,Boxer LA,Warren RW,Conley ME,Ferrara J,Leavitt RY,Fauci AS,Taylor BA

    更新日期:1987-11-01 00:00:00

  • Homologies between human and marmoset (Callithrix jacchus) chromosomes revealed by comparative chromosome painting.

    abstract::Regions of DNA homology between human and marmoset (Callithrix jacchus) chromosomes have been demonstrated using fluorescence in situ hybridization. All 24 chromosome paints and two centromere repeat sequences from Homo sapiens (HSA) have been annealed to previously G-banded metaphase spreads of Callithrix jacchus. Al...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1996.0186

    authors: Sherlock JK,Griffin DK,Delhanty JD,Parrington JM

    更新日期:1996-04-15 00:00:00

  • Localization of the properdin structural locus to Xp11.23-Xp21.1.

    abstract::Properdin is a serum protein belonging to the alternative pathway of complement activation whose absence is often associated with fatal bacterial infections. Properdin deficiency segregates with an X-linked recessive pattern and its position has been recently refined by genetic linkage analysis to the proximal part of...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(89)90085-2

    authors: Goundis D,Holt SM,Boyd Y,Reid KB

    更新日期:1989-07-01 00:00:00

  • Isolation and characterization of a novel human paired-like homeodomain-containing transcription factor gene, VSX1, expressed in ocular tissues.

    abstract::Homeodomain transcription factors control cell fates during the development of all animals. The paired-like subfamily of homeodomain proteins has been particularly implicated in ocular development in different species. In this paper we report the cDNA sequence, genomic structure, localization, and expression data of a...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1999.6093

    authors: Semina EV,Mintz-Hittner HA,Murray JC

    更新日期:2000-01-15 00:00:00

  • A genome survey for novel Alzheimer disease risk loci: results at 10-cM resolution.

    abstract::We completed a systematic survey of the human genome, conducted at an average resolution of 10 cM, for the identification of simple sequence tandem repeat polymorphisms (SSTRPs) that target new risk genes for Alzheimer disease (AD) by virtue of linkage disequilibrium. The efficiency of our association study was enhanc...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1006/geno.1998.5306

    authors: Zubenko GS,Hughes HB,Stiffler JS,Hurtt MR,Kaplan BB

    更新日期:1998-06-01 00:00:00

  • Isolation of a human chromosome 14-only somatic cell hybrid: analysis using Alu and LINE-based PCR.

    abstract::Interspecific somatic cell hybrids containing single human chromosomes are valuable reagents for localization of cloned genes and DNA fragments to specific chromosomes, for the development of chromosome-specific libraries, and for generation of hybrid cell lines containing subchromosomal regions. A CHO somatic cell hy...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/0888-7543(91)90122-u

    authors: Mares A Jr,Ledbetter SA,Ledbetter DH,Roberts R,Hejtmancik JF

    更新日期:1991-09-01 00:00:00

  • Odorant and vomeronasal receptor genes in two mouse genome assemblies.

    abstract::Odorant receptors (ORs) and vomeronasal receptors (V1Rs and V2Rs) are large superfamilies of chemosensory receptors. As an extension of previous research using the 2001 Celera mouse genome assembly, we analyzed OR and V1R genes in the 2002 public mouse genome assembly. We identified 1403 OR genes (1068 potentially int...

    journal_title:Genomics

    pub_type: 杂志文章

    doi:10.1016/j.ygeno.2003.10.009

    authors: Zhang X,Rodriguez I,Mombaerts P,Firestein S

    更新日期:2004-05-01 00:00:00