PlanTE-MIR DB: a database for transposable element-related microRNAs in plant genomes
Autor(a) principal: | |
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Data de Publicação: | 2016 |
Outros Autores: | , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1007/s10142-016-0480-5 http://hdl.handle.net/11449/168608 |
Resumo: | Transposable elements (TEs) comprise a major fraction of many plant genomes and are known to drive their organization and evolution. Several studies show that these repetitive elements have a prominent role in shaping noncoding regions of the genome such as microRNA (miRNA) loci, which are components of post-transcriptional regulation mechanisms. Although some studies have reported initial formation of miRNA loci from TE sequences, especially in model plants, the approaches that were used did not employ systems that would allow results to be delivered by a user-friendly database. In this study, we identified 152 precursor miRNAs overlapping TEs in 10 plant species. PlanTE-MIR DB was designed to assemble this data and deliver it to the scientific community interested in miRNA origin, evolution, and regulation pathways. Users can browse the database through a web interface and search for entries using various parameters. This resource is cross-referenced with repetitive element (Repbase Update) and miRNA (miRBase) repositories, where sequences can be checked for further analysis. All data in PlanTE-MIR DB are publicly available for download in several file formats to facilitate their understanding and use. The database is hosted at http://bioinfo-tool.cp.utfpr.edu.br/plantemirdb/. |
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PlanTE-MIR DB: a database for transposable element-related microRNAs in plant genomesDatabaseMicroRNAsPlant genomesTransposable elementsTransposable elements (TEs) comprise a major fraction of many plant genomes and are known to drive their organization and evolution. Several studies show that these repetitive elements have a prominent role in shaping noncoding regions of the genome such as microRNA (miRNA) loci, which are components of post-transcriptional regulation mechanisms. Although some studies have reported initial formation of miRNA loci from TE sequences, especially in model plants, the approaches that were used did not employ systems that would allow results to be delivered by a user-friendly database. In this study, we identified 152 precursor miRNAs overlapping TEs in 10 plant species. PlanTE-MIR DB was designed to assemble this data and deliver it to the scientific community interested in miRNA origin, evolution, and regulation pathways. Users can browse the database through a web interface and search for entries using various parameters. This resource is cross-referenced with repetitive element (Repbase Update) and miRNA (miRBase) repositories, where sequences can be checked for further analysis. All data in PlanTE-MIR DB are publicly available for download in several file formats to facilitate their understanding and use. The database is hosted at http://bioinfo-tool.cp.utfpr.edu.br/plantemirdb/.Graduation Program in Genetics and Molecular Biology Universidade Estadual de LondrinaBioinformatics Laboratory Universidade Tecnológica Federal do Paraná UTFPRDepartment of Botany Instituto de Biociências Universidade Estadual Paulista UNESPDepartment of Botany Instituto de Biociências Universidade Estadual Paulista UNESPUniversidade Estadual de Londrina (UEL)UTFPRUniversidade Estadual Paulista (Unesp)R. Lorenzetti, Alan P.A. de Antonio, Gabriel Y.Paschoal, Alexandre R.Domingues, Douglas S. [UNESP]2018-12-11T16:42:09Z2018-12-11T16:42:09Z2016-05-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article235-242application/pdfhttp://dx.doi.org/10.1007/s10142-016-0480-5Functional and Integrative Genomics, v. 16, n. 3, p. 235-242, 2016.1438-79481438-793Xhttp://hdl.handle.net/11449/16860810.1007/s10142-016-0480-52-s2.0-849647618192-s2.0-84964761819.pdfScopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengFunctional and Integrative Genomics1,410info:eu-repo/semantics/openAccess2023-11-01T06:12:33Zoai:repositorio.unesp.br:11449/168608Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T16:37:54.829389Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
PlanTE-MIR DB: a database for transposable element-related microRNAs in plant genomes |
title |
PlanTE-MIR DB: a database for transposable element-related microRNAs in plant genomes |
spellingShingle |
PlanTE-MIR DB: a database for transposable element-related microRNAs in plant genomes R. Lorenzetti, Alan P. Database MicroRNAs Plant genomes Transposable elements |
title_short |
PlanTE-MIR DB: a database for transposable element-related microRNAs in plant genomes |
title_full |
PlanTE-MIR DB: a database for transposable element-related microRNAs in plant genomes |
title_fullStr |
PlanTE-MIR DB: a database for transposable element-related microRNAs in plant genomes |
title_full_unstemmed |
PlanTE-MIR DB: a database for transposable element-related microRNAs in plant genomes |
title_sort |
PlanTE-MIR DB: a database for transposable element-related microRNAs in plant genomes |
author |
R. Lorenzetti, Alan P. |
author_facet |
R. Lorenzetti, Alan P. A. de Antonio, Gabriel Y. Paschoal, Alexandre R. Domingues, Douglas S. [UNESP] |
author_role |
author |
author2 |
A. de Antonio, Gabriel Y. Paschoal, Alexandre R. Domingues, Douglas S. [UNESP] |
author2_role |
author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual de Londrina (UEL) UTFPR Universidade Estadual Paulista (Unesp) |
dc.contributor.author.fl_str_mv |
R. Lorenzetti, Alan P. A. de Antonio, Gabriel Y. Paschoal, Alexandre R. Domingues, Douglas S. [UNESP] |
dc.subject.por.fl_str_mv |
Database MicroRNAs Plant genomes Transposable elements |
topic |
Database MicroRNAs Plant genomes Transposable elements |
description |
Transposable elements (TEs) comprise a major fraction of many plant genomes and are known to drive their organization and evolution. Several studies show that these repetitive elements have a prominent role in shaping noncoding regions of the genome such as microRNA (miRNA) loci, which are components of post-transcriptional regulation mechanisms. Although some studies have reported initial formation of miRNA loci from TE sequences, especially in model plants, the approaches that were used did not employ systems that would allow results to be delivered by a user-friendly database. In this study, we identified 152 precursor miRNAs overlapping TEs in 10 plant species. PlanTE-MIR DB was designed to assemble this data and deliver it to the scientific community interested in miRNA origin, evolution, and regulation pathways. Users can browse the database through a web interface and search for entries using various parameters. This resource is cross-referenced with repetitive element (Repbase Update) and miRNA (miRBase) repositories, where sequences can be checked for further analysis. All data in PlanTE-MIR DB are publicly available for download in several file formats to facilitate their understanding and use. The database is hosted at http://bioinfo-tool.cp.utfpr.edu.br/plantemirdb/. |
publishDate |
2016 |
dc.date.none.fl_str_mv |
2016-05-01 2018-12-11T16:42:09Z 2018-12-11T16:42:09Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1007/s10142-016-0480-5 Functional and Integrative Genomics, v. 16, n. 3, p. 235-242, 2016. 1438-7948 1438-793X http://hdl.handle.net/11449/168608 10.1007/s10142-016-0480-5 2-s2.0-84964761819 2-s2.0-84964761819.pdf |
url |
http://dx.doi.org/10.1007/s10142-016-0480-5 http://hdl.handle.net/11449/168608 |
identifier_str_mv |
Functional and Integrative Genomics, v. 16, n. 3, p. 235-242, 2016. 1438-7948 1438-793X 10.1007/s10142-016-0480-5 2-s2.0-84964761819 2-s2.0-84964761819.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Functional and Integrative Genomics 1,410 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
235-242 application/pdf |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1808128680854028288 |