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Camargo AA, Samaia HP, Dias-Neto E, Simão DF, Migotto IA, Briones MR, Costa FF, Nagai MA, Verjovski-Almeida S, Zago MA, Andrade LE, Carrer H, El-Dorry HF, Espreafico EM, Habr-Gama A, Giannella-Neto D, Goldman GH, Gruber A, Hackel C, Kimura ET, Maciel RM, Marie SK, Martins EA, Nobrega MP, Paco-Larson ML, Pardini MI, Pereira GG, Pesquero JB, Rodrigues V, Rogatto SR, da Silva ID, Sogayar MC, Sonati MF, Tajara EH, Valentini SR, Alberto FL, Amaral ME, Aneas I, Arnaldi LA, de Assis AM, Bengtson MH, Bergamo NA, Bombonato V, de Camargo ME, Canevari RA, Carraro DM, Cerutti JM, Correa ML, Correa RF, Costa MC, Curcio C, Hokama PO, Ferreira AJ, Furuzawa GK, Gushiken T, Ho PL, Kimura E, Krieger JE, Leite LC, Majumder P, Marins M, Marques ER, Melo AS, Melo MB, Mestriner CA, Miracca EC, Miranda DC, Nascimento AL, Nobrega FG, Ojopi EP, Pandolfi JR, Pessoa LG, Prevedel AC, Rahal P, Rainho CA, Reis EM, Ribeiro ML, da Ros N, de Sa RG, Sales MM, Sant'anna SC, dos Santos ML, da Silva AM, da Silva NP, Silva WA, da Silveira RA, Sousa JF, Stecconi D, Tsukumo F, Valente V, Soares F, Moreira ES, Nunes DN, Correa RG, Zalcberg H, Carvalho AF, Reis LF, Brentani RR, Simpson AJ, de Souza SJ, Melo M. The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome. Proc Natl Acad Sci U S A 2001; 98:12103-8. [PMID: 11593022 PMCID: PMC59775 DOI: 10.1073/pnas.201182798] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Open reading frame expressed sequences tags (ORESTES) differ from conventional ESTs by providing sequence data from the central protein coding portion of transcripts. We generated a total of 696,745 ORESTES sequences from 24 human tissues and used a subset of the data that correspond to a set of 15,095 full-length mRNAs as a means of assessing the efficiency of the strategy and its potential contribution to the definition of the human transcriptome. We estimate that ORESTES sampled over 80% of all highly and moderately expressed, and between 40% and 50% of rarely expressed, human genes. In our most thoroughly sequenced tissue, the breast, the 130,000 ORESTES generated are derived from transcripts from an estimated 70% of all genes expressed in that tissue, with an equally efficient representation of both highly and poorly expressed genes. In this respect, we find that the capacity of the ORESTES strategy both for gene discovery and shotgun transcript sequence generation significantly exceeds that of conventional ESTs. The distribution of ORESTES is such that many human transcripts are now represented by a scaffold of partial sequences distributed along the length of each gene product. The experimental joining of the scaffold components, by reverse transcription-PCR, represents a direct route to transcript finishing that may represent a useful alternative to full-length cDNA cloning.
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Affiliation(s)
- A A Camargo
- Ludwig Institute for Cancer Research, 01509-010, São Paulo, Brazil
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de Souza SJ, Camargo AA, Briones MR, Costa FF, Nagai MA, Verjovski-Almeida S, Zago MA, Andrade LE, Carrer H, El-Dorry HF, Espreafico EM, Habr-Gama A, Giannella-Neto D, Goldman GH, Gruber A, Hackel C, Kimura ET, Maciel RM, Marie SK, Martins EA, Nobrega MP, Paco-Larson ML, Pardini MI, Pereira GG, Pesquero JB, Rodrigues V, Rogatto SR, da Silva ID, Sogayar MC, de Fátima Sonati M, Tajara EH, Valentini SR, Acencio M, Alberto FL, Amaral ME, Aneas I, Bengtson MH, Carraro DM, Carvalho AF, Carvalho LH, Cerutti JM, Corrêa ML, Costa MC, Curcio C, Gushiken T, Ho PL, Kimura E, Leite LC, Maia G, Majumder P, Marins M, Matsukuma A, Melo AS, Mestriner CA, Miracca EC, Miranda DC, Nascimento AN, Nóbrega FG, Ojopi EP, Pandolfi JR, Pessoa LG, Rahal P, Rainho CA, da Rós N, de Sá RG, Sales MM, da Silva NP, Silva TC, da Silva W, Simão DF, Sousa JF, Stecconi D, Tsukumo F, Valente V, Zalcbeg H, Brentani RR, Reis FL, Dias-Neto E, Simpson AJ. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags. Proc Natl Acad Sci U S A 2000; 97:12690-3. [PMID: 11070084 PMCID: PMC18825 DOI: 10.1073/pnas.97.23.12690] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1, 181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. Of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTES coincided with DNA regions predicted as encoding exons by genscan. (http://genes.mit.edu/GENSCAN.html).
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Affiliation(s)
- S J de Souza
- Ludwig Institute for Cancer Research, São Paulo 01509-010, SP, Brazil
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