GSDS 2.0: an upgraded gene feature visualization server

Hu, Bo; Jin, Jinpu; Guo, An‐Yuan; Zhang, He; Luo, Jingchu; Gao, Ge

doi:10.1093/bioinformatics/btu817

Cited by 3,255 publications

(2,113 citation statements)

References 13 publications

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“…Additionally, all of the identified motifs were annotated using InterProScan (http://www.ebi.ac.uk/interpro/search/sequence-search). The exon/intron structures of the SiWRKY genes were determined by comparing their predicted coding sequence (CDS) with genomic sequences using the gene structure display server web-based bioinformatics tool (http://gsds.cbi.pku.edu.cn/) [58].…”

Section: Protein Properties and Sequence Analysismentioning

confidence: 99%

Genome-wide analysis of WRKY gene family in the sesame genome and identification of the WRKY genes involved in responses to abiotic stresses

Liu

et al. 2017

BMC Plant Biol

111

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Background: Sesame (Sesamum indicum L.) is one of the world's most important oil crops. However, it is susceptible to abiotic stresses in general, and to waterlogging and drought stresses in particular. The molecular mechanisms of abiotic stress tolerance in sesame have not yet been elucidated. The WRKY domain transcription factors play significant roles in plant growth, development, and responses to stresses. However, little is known about the number, location, structure, molecular phylogenetics, and expression of the WRKY genes in sesame.

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Section: Protein Properties and Sequence Analysismentioning

confidence: 99%

Genome-wide analysis of WRKY gene family in the sesame genome and identification of the WRKY genes involved in responses to abiotic stresses

Liu

et al. 2017

BMC Plant Biol

111

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“…The exon-intron number and gene architecture of the identified GST genes were obtained using Gene Structure Display Server 2.0 (GSDS; http://gsds.cbi.pku.edu.cn/) by aligning the FASTA formatted CDS and genomic DNA sequences (Hu et al 2015).…”

Section: Gene Structure Visualizationmentioning

confidence: 99%

In silico genome-wide identification and characterization of the glutathione S-transferase gene family in Vigna radiata

Vaish

Awasthi

Tiwari

et al. 2018

Genome

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Plant glutathione S-transferases are integral to normal plant metabolism, and biotic and abiotic stress tolerance. GST gene family has been characterized in diverse plant species using molecular biology and bioinformatics approaches. In the current study, in silico analysis identified 44 GSTs in Vigna radiata. Of the total 44 GSTs identified, chromosomal locations of 31 GSTs were confirmed. The pI value of GST proteins ranged from 5.10 to 9.40. The predicted molecular weights ranged from 13.12 to 50 kDa. Subcellular localization analysis revealed that all GSTs were predominantly localized in the cytoplasm. The active site amino acids were confirmed to be serine in tau, phi, theta, zeta and TCHQD; cysteine in lambda, DHAR and omega; and tyrosine in EF1G. The gene architecture conformed to the 2 exon-1 intron and 3 exon-2 intron organization in case of tau and phi classes, respectively. MEME analysis identified 10 significantly conserved motifs with the width of 8 to 50 amino acids. The motifs identified were either specific to a specific GST class, or were shared by multiple GST classes. The results of the current study will be of potential importance in the characterization of GST gene family in V. radiata, an economically important leguminous crop.

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“…The gene structure and intron-phase analyses were carried out using the software Gene Structure Display Server 2.0 (GSDS2.0) (Hu et al 2015).…”

Section: Gene Structure Analysismentioning

confidence: 99%

Identification, duplication, evolution and expression analyses of caleosins in Brassica plants and Arabidopsis subspecies

et al. 2016

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Vous avez des questions? Nous pouvons vous aider. Pour communiquer directement avec un auteur, consultez la première page de la revue dans laquelle son article a été publié afin de trouver ses coordonnées. Si vous n'arrivez pas à les repérer, communiquez avec nous à PublicationsArchive-ArchivesPublications@nrc-cnrc.gc.ca. Questions? Contact the NRC Publications Archive team atPublicationsArchive-ArchivesPublications@nrc-cnrc.gc.ca. If you wish to email the authors directly, please see the first page of the publication for their contact information. NRC Publications Archive Archives des publications du CNRCThis publication could be one of several versions: author's original, accepted manuscript or the publisher's version. / La version de cette publication peut être l'une des suivantes : la version prépublication de l'auteur, la version acceptée du manuscrit ou la version de l'éditeur. NRC Publications Record / Notice d'Archives des publications de CNRC:http://nparc.cisti-icist.nrc-cnrc.gc.ca/eng/view/object/?id=f37a8f5d-b46d-49f5-ba0f-e42c14b87a96 http://nparc.cisti-icist.nrc-cnrc.gc.ca/fra/voir/objet/?id=f37a8f5d-b46d-49f5-ba0f-e42c14b87a96 the first time. Segmental duplication was the main form of gene expansion. Alignment, motif and phylogenetic analyses showed that Brassica caleosins belong to either the H-family or the L-family with different motif structures and physicochemical properties. Our findings strongly suggest that L-caleosins are evolved from H-caleosins. Predicted phosphorylation sites were differentially conserved in H-caleosin and L-caleosins, respectively. 'RY-repeat' elements and phytohormone-related cis-elements were identified in different caleosins, which suggest diverse physiological functions. Gene structure analysis indicated that most caleosins (38 out of 44) contained six exons and five introns and their intron phases were highly conserved. Structurally integrated caleosins, such as BrCLO3-3 and BrCLO4-2, showed high expression levels and may have important roles. Some caleosins, such as BrCLO2 and BoCLO8-2, lost motifs of the calcium binding domain, proline knot, potential phosphorylation sites and haem-binding sites. Combined with their low expression, it is suggested that these caleosins may have lost function. 1 3 Mol Genet Genomics DOI 10.1007/s00438-015-1156- Abstract

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GSDS 2.0: an upgraded gene feature visualization server

Cited by 3,255 publications

References 13 publications

Genome-wide analysis of WRKY gene family in the sesame genome and identification of the WRKY genes involved in responses to abiotic stresses

Genome-wide analysis of WRKY gene family in the sesame genome and identification of the WRKY genes involved in responses to abiotic stresses

In silico genome-wide identification and characterization of the glutathione S-transferase gene family in Vigna radiata

Identification, duplication, evolution and expression analyses of caleosins in Brassica plants and Arabidopsis subspecies

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