Genome organization of the SARS-CoV.
Identifieur interne : 000C91 ( Ncbi/Merge ); précédent : 000C90; suivant : 000C92Genome organization of the SARS-CoV.
Auteurs : Jing Xu [République populaire de Chine] ; Jianfei Hu ; Jing Wang ; Yujun Han ; Yongwu Hu ; Jie Wen ; Yan Li ; Jia Ji ; Jia Ye ; Zizhang Zhang ; Wei Wei ; Songgang Li ; Jun Wang ; Jian Wang ; Jun Yu ; Huanming YangSource :
- Genomics, proteomics & bioinformatics [ 1672-0229 ] ; 2003.
Descripteurs français
- KwdFr :
- Analyse de séquence, Biologie informatique (), Cadres ouverts de lecture, Composition en bases nucléiques, Données de séquences moléculaires, Génome viral, Masse moléculaire, Modèles génétiques, Point isoélectrique, Substitution d'acide aminé, Séquence nucléotidique, Transcription génétique, Virus du SRAS (génétique).
- MESH :
- génétique : Virus du SRAS.
- Analyse de séquence, Biologie informatique, Cadres ouverts de lecture, Composition en bases nucléiques, Données de séquences moléculaires, Génome viral, Masse moléculaire, Modèles génétiques, Point isoélectrique, Substitution d'acide aminé, Séquence nucléotidique, Transcription génétique.
English descriptors
- KwdEn :
- MESH :
Abstract
Annotation of the genome sequence of the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) is indispensable to understand its evolution and pathogenesis. We have performed a full annotation of the SARS-CoV genome sequences by using annotation programs publicly available or developed by ourselves. Totally, 21 open reading frames (ORFs) of genes or putative uncharacterized proteins (PUPs) were predicted. Seven PUPs had not been reported previously, and two of them were predicted to contain transmembrane regions. Eight ORFs partially overlapped with or embedded into those of known genes, revealing that the SARS-CoV genome is a small and compact one with overlapped coding regions. The most striking discovery is that an ORF locates on the minus strand. We have also annotated non-coding regions and identified the transcription regulating sequences (TRS) in the intergenic regions. The analysis of TRS supports the minus strand extending transcription mechanism of coronavirus. The SNP analysis of different isolates reveals that mutations of the sequences do not affect the prediction results of ORFs.
DOI: 10.1016/s1672-0229(03)01028-3
PubMed: 15629035
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 002974
- to stream PubMed, to step Curation: 002974
- to stream PubMed, to step Checkpoint: 003236
Links to Exploration step
pubmed:15629035Le document en format XML
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<front><div type="abstract" xml:lang="en">Annotation of the genome sequence of the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) is indispensable to understand its evolution and pathogenesis. We have performed a full annotation of the SARS-CoV genome sequences by using annotation programs publicly available or developed by ourselves. Totally, 21 open reading frames (ORFs) of genes or putative uncharacterized proteins (PUPs) were predicted. Seven PUPs had not been reported previously, and two of them were predicted to contain transmembrane regions. Eight ORFs partially overlapped with or embedded into those of known genes, revealing that the SARS-CoV genome is a small and compact one with overlapped coding regions. The most striking discovery is that an ORF locates on the minus strand. We have also annotated non-coding regions and identified the transcription regulating sequences (TRS) in the intergenic regions. The analysis of TRS supports the minus strand extending transcription mechanism of coronavirus. The SNP analysis of different isolates reveals that mutations of the sequences do not affect the prediction results of ORFs.</div>
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<ReferenceList><Reference><Citation>EMBO J. 2001 Dec 17;20(24):7220-8</Citation>
<ArticleIdList><ArticleId IdType="pubmed">11742998</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
<ReferenceList><Reference><Citation>J Virol. 2000 Jun;74(11):5053-65</Citation>
<ArticleIdList><ArticleId IdType="pubmed">10799579</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
</PubmedData>
</pubmed>
<affiliations><list><country><li>République populaire de Chine</li>
</country>
<settlement><li>Pékin</li>
</settlement>
</list>
<tree><noCountry><name sortKey="Han, Yujun" sort="Han, Yujun" uniqKey="Han Y" first="Yujun" last="Han">Yujun Han</name>
<name sortKey="Hu, Jianfei" sort="Hu, Jianfei" uniqKey="Hu J" first="Jianfei" last="Hu">Jianfei Hu</name>
<name sortKey="Hu, Yongwu" sort="Hu, Yongwu" uniqKey="Hu Y" first="Yongwu" last="Hu">Yongwu Hu</name>
<name sortKey="Ji, Jia" sort="Ji, Jia" uniqKey="Ji J" first="Jia" last="Ji">Jia Ji</name>
<name sortKey="Li, Songgang" sort="Li, Songgang" uniqKey="Li S" first="Songgang" last="Li">Songgang Li</name>
<name sortKey="Li, Yan" sort="Li, Yan" uniqKey="Li Y" first="Yan" last="Li">Yan Li</name>
<name sortKey="Wang, Jian" sort="Wang, Jian" uniqKey="Wang J" first="Jian" last="Wang">Jian Wang</name>
<name sortKey="Wang, Jing" sort="Wang, Jing" uniqKey="Wang J" first="Jing" last="Wang">Jing Wang</name>
<name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name>
<name sortKey="Wei, Wei" sort="Wei, Wei" uniqKey="Wei W" first="Wei" last="Wei">Wei Wei</name>
<name sortKey="Wen, Jie" sort="Wen, Jie" uniqKey="Wen J" first="Jie" last="Wen">Jie Wen</name>
<name sortKey="Yang, Huanming" sort="Yang, Huanming" uniqKey="Yang H" first="Huanming" last="Yang">Huanming Yang</name>
<name sortKey="Ye, Jia" sort="Ye, Jia" uniqKey="Ye J" first="Jia" last="Ye">Jia Ye</name>
<name sortKey="Yu, Jun" sort="Yu, Jun" uniqKey="Yu J" first="Jun" last="Yu">Jun Yu</name>
<name sortKey="Zhang, Zizhang" sort="Zhang, Zizhang" uniqKey="Zhang Z" first="Zizhang" last="Zhang">Zizhang Zhang</name>
</noCountry>
<country name="République populaire de Chine"><noRegion><name sortKey="Xu, Jing" sort="Xu, Jing" uniqKey="Xu J" first="Jing" last="Xu">Jing Xu</name>
</noRegion>
</country>
</tree>
</affiliations>
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