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Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

2000; National Academy of Sciences; Volume: 97; Issue: 23 Linguagem: Inglês

10.1073/pnas.97.23.12690

1091-6490

Sandro J. de Souza, Anamaria A. Camargo, Marcelo R. S. Briones, Fernando Ferreira Costa, María Aparecida Nagai, Sérgio Verjovski-Almeida, Marco A. Zago, Luís Eduardo Coelho Andrade, Helaine Carrer, Hamza El‐Dorry, Enilza Maria Espreáfico, Angelita Habr‐Gama, Daniel Giannella‐Neto, Gustavo H. Goldman, Arthur Gruber, Christine Hackel, Edna Teruko Kimura, Rui M. B. Maciel, Suely Kazue Nagahashi Marie, Elizabeth A. L. Martins, Marina P. Nóbrega, Maria Luisa Paçó‐Larson, Maria Inês de Moura Campos Pardini, Gonçalo G. Pereira, João Bosco Pesquero, Vanderlei Rodrigues, Sílvia Regina Rogatto, Ismael Dale Cotrim Guerreiro da Silva, Mari Cleide Sogayar, María de Fátima Sonati, Eloíza H. Tajara, Sandro Roberto Valentini, Márcio Luís Acencio, Fernando Alberto, M.E.J. Amaral, Ivy Aneas, Mário Henrique Bengtson, Dirce Maria Carraro, Alex F. Carvalho, Lucia Helena de Carvalho, Janete M. Cerutti, Maria Lúcia Corrêa‐Giannella, María Costa, Cyntia Curcio, Tsieko Gushiken, Paulo Lee Ho, Elza Kimura, Luciana C. C. Leite, Gustavo Maia, Paromita Majumder, Mozart Marins, Adriana Yamaguti Matsukuma, Analy Salles de Azevedo Melo, Carlos Alberto Mestriner, Elisabete Miracca, Daniela C. Miranda, Ana L. T. O. Nascimento, Francisco G. Nóbrega, Elida P.B. Ojopi, J. R. C. Pandolfi, Luciana Gilbert Pessoa, Paula Rahal, Cláudia Aparecida Rainho, Nancy da Rós, Renata Guerra de Sá, Magaly M. Sales, Neusa P. da Silva, Tereza C. Silva, Wilson A. Silva, Daniel Simão, Josane F. Sousa, Daniella Stecconi, Fernando Tsukumo, Valéria Valente, Heloisa Zalcberg, Helena Brentani, Luiz F. L. Reis, Emmanuel Dias‐Neto, Andrew J.G. Simpson,

Genomics and Chromatin Dynamics

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 ).