A transcript finishing initiative for closing gaps in the human transcriptome.
Autor(a) principal: | |
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Data de Publicação: | 2004 |
Outros Autores: | |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UFOP |
Texto Completo: | http://www.repositorio.ufop.br/handle/123456789/4614 https://doi.org/10.1101/gr.2111304 |
Resumo: | We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST clusters, mapped against the genomic sequence. Each pair of EST clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1% was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms. |
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Sogayar, Mari CleideCamargo, Anamaria Aranha2015-03-12T18:54:04Z2015-03-12T18:54:04Z2004SOGAYAR, M. C.; CAMARGO, A. A. A transcript finishing initiative for closing gaps in the human transcriptome. Genome Research, v. 14, n.7, p. 1413-1423, 2004. Disponível em: <http://genome.cshlp.org/content/14/7/1413.long>. Acesso em: 08 nov. 2014.1549-5469http://www.repositorio.ufop.br/handle/123456789/4614https://doi.org/10.1101/gr.2111304We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST clusters, mapped against the genomic sequence. Each pair of EST clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1% was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms.A transcript finishing initiative for closing gaps in the human transcriptome.info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleAfter six months, the articles are available under a Creative Commons License (Attribution-NonCommercial 4.0 International License). Fonte Genome Research. Acesso em: 12 jan. 2014.info:eu-repo/semantics/openAccessengreponame:Repositório Institucional da UFOPinstname:Universidade Federal de Ouro Preto (UFOP)instacron:UFOPLICENSElicense.txtlicense.txttext/plain; charset=utf-82636http://www.repositorio.ufop.br/bitstream/123456789/4614/2/license.txtc2ffdd99e58acf69202dff00d361f23aMD52ORIGINALARTIGO_TranscriptFinishingInitiative.pdfARTIGO_TranscriptFinishingInitiative.pdfapplication/pdf366334http://www.repositorio.ufop.br/bitstream/123456789/4614/1/ARTIGO_TranscriptFinishingInitiative.pdf702428a05e3731732ff2f7bc3a769225MD51123456789/46142019-06-24 14:35:00.366oai:localhost: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Repositório InstitucionalPUBhttp://www.repositorio.ufop.br/oai/requestrepositorio@ufop.edu.bropendoar:32332019-06-24T18:35Repositório Institucional da UFOP - Universidade Federal de Ouro Preto (UFOP)false |
dc.title.pt_BR.fl_str_mv |
A transcript finishing initiative for closing gaps in the human transcriptome. |
title |
A transcript finishing initiative for closing gaps in the human transcriptome. |
spellingShingle |
A transcript finishing initiative for closing gaps in the human transcriptome. Sogayar, Mari Cleide |
title_short |
A transcript finishing initiative for closing gaps in the human transcriptome. |
title_full |
A transcript finishing initiative for closing gaps in the human transcriptome. |
title_fullStr |
A transcript finishing initiative for closing gaps in the human transcriptome. |
title_full_unstemmed |
A transcript finishing initiative for closing gaps in the human transcriptome. |
title_sort |
A transcript finishing initiative for closing gaps in the human transcriptome. |
author |
Sogayar, Mari Cleide |
author_facet |
Sogayar, Mari Cleide Camargo, Anamaria Aranha |
author_role |
author |
author2 |
Camargo, Anamaria Aranha |
author2_role |
author |
dc.contributor.author.fl_str_mv |
Sogayar, Mari Cleide Camargo, Anamaria Aranha |
description |
We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST clusters, mapped against the genomic sequence. Each pair of EST clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1% was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms. |
publishDate |
2004 |
dc.date.issued.fl_str_mv |
2004 |
dc.date.accessioned.fl_str_mv |
2015-03-12T18:54:04Z |
dc.date.available.fl_str_mv |
2015-03-12T18:54:04Z |
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.citation.fl_str_mv |
SOGAYAR, M. C.; CAMARGO, A. A. A transcript finishing initiative for closing gaps in the human transcriptome. Genome Research, v. 14, n.7, p. 1413-1423, 2004. Disponível em: <http://genome.cshlp.org/content/14/7/1413.long>. Acesso em: 08 nov. 2014. |
dc.identifier.uri.fl_str_mv |
http://www.repositorio.ufop.br/handle/123456789/4614 |
dc.identifier.issn.none.fl_str_mv |
1549-5469 |
dc.identifier.doi.none.fl_str_mv |
https://doi.org/10.1101/gr.2111304 |
identifier_str_mv |
SOGAYAR, M. C.; CAMARGO, A. A. A transcript finishing initiative for closing gaps in the human transcriptome. Genome Research, v. 14, n.7, p. 1413-1423, 2004. Disponível em: <http://genome.cshlp.org/content/14/7/1413.long>. Acesso em: 08 nov. 2014. 1549-5469 |
url |
http://www.repositorio.ufop.br/handle/123456789/4614 https://doi.org/10.1101/gr.2111304 |
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eng |
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eng |
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openAccess |
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