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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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