title: Genome organization of the SARS-CoV.
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.
authors.affiliation: Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Xu
authors.forename: Jianfei
authors.initials: J
authors.lastname: Hu
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.forename: Yujun
authors.initials: Y
authors.lastname: Han
authors.forename: Yongwu
authors.initials: Y
authors.lastname: Hu
authors.forename: Jie
authors.initials: J
authors.lastname: Wen
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.forename: Jia
authors.initials: J
authors.lastname: Ji
authors.forename: Jia
authors.initials: J
authors.lastname: Ye
authors.forename: Zizhang
authors.initials: Z
authors.lastname: Zhang
authors.forename: Wei
authors.initials: W
authors.lastname: Wei
authors.forename: Songgang
authors.initials: S
authors.lastname: Li
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
mesh_terms: D019943:Amino Acid Substitution; D001482:Base Composition; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D016679:Genome, Viral; D007526:Isoelectric Point; D008957:Models, Genetic; D008969:Molecular Sequence Data; D008970:Molecular Weight; D016366:Open Reading Frames; D045473:Severe acute respiratory syndrome-related coronavirus / Q000235:genetics*; D017421:Sequence Analysis; D014158:Transcription, Genetic