Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags
Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags
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DOI：
10.1073/pnas.97.23.12690
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发表时间：
2000-11-07
影响因子：
11.1
通讯作者：
Simpson, AJG
中科院分区：
文献类型：
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作者：
de Souza, SJ;Camargo, AA;Simpson, AJG
人类基因组中的转录序列只能通过与由天然存在的mRNA合成的cDNA衍生的序列进行比对来确定。我们构建了一组250，000个cDNA，这些cDNA代表部分表达的基因序列，并且偏向于所得转录物的中心编码区。它们被称为ORF表达序列标签（ORESTES）。将250，000个ORESTE组装成81，429个重叠群。其中，1,181个（1.45%）被发现与22号染色体上的247个已知基因中的162个（65.6%）、150个相关基因中的67个（44.6%）和148个EST预测基因中的45个（30.4%）的至少一个ORESTES重叠群匹配。使用一组严格的标准来验证我们的序列，我们在22号染色体上进一步鉴定了219个先前未注释的转录序列。其中，171个事实上也由GenBank中可获得的EST或全长cDNA序列定义，但未用于第一个人类染色体序列的初始注释。因此，尽管在本分析时，在公共数据库中所有表达的人类序列中占不到15%，但ORESTE序列在22号染色体上定义了48个未被其他序列定义的转录序列。ORESTEs定义的所有转录序列与GENSCAN预测的编码外显子的DNA区域一致。
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.