The developmentally active and cell-stress responsive hsrω locus in Drosophila melanogaster carries two exons, one omega intron, one short translatable open reading frame (ORFω), long stretch of unique tandem repeats and an overlapping mir-4951 near its 3′ end. It produces multiple long noncoding RNAs (lncRNAs) using two transcription start and four termination sites. Earlier cytogenetic studies revealed functional conservation of hsrω in several Drosophila species. However, sequence analysis in three species showed poor conservation for ORFω, tandem repeat and other regions while the 16 nt at 5′ and 60 nt at 3′ splice junctions of the omega intron, respectively, were found to be ultra-conserved. The present bioinformatic study using the splice-junction landmarks in D. melanogaster hsrω identified orthologues in publicly available 34 Drosophila species genomes. Each orthologue carries a short ORFω, ultra-conserved splice junctions of omega intron, repeat region, conserved 3′-end located at mir-4951, and syntenic neighbours. Multiple copies of conserved nonamer motifs are seen in the tandem repeat region, despite a high variability in the repeat sequences. Intriguingly, only the omega intron sequences in different species show evolutionary relationships matching the general phylogenetic history in the genus. Search in other known insect genomes did not reveal sequence homology although a locus with similar functional properties is suggested in Chironomus and Ceratitis genera. Amidst the high sequence divergence, the conserved organization of exons, ORFω and omega intron in this gene’s proximal part and tandem repeats in distal part across the Drosophila genus is remarkable and possibly reflects functional importance of higher order structure of hsrω lncRNAs and the small omega peptide.

中文翻译：

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果蝇属 hsrω lncRNA 基因序列差异中基因结构和域的保护：计算机分析

黑腹果蝇中发育活跃和细胞应激反应的 hsrω 基因座携带两个外显子，一个 omega 内含子，一个短的可翻译开放阅读框 (ORFω)，长一段独特的串联重复序列和一个重叠的 mir-4951 靠近其 3' 端。它使用两个转录起始位点和四个终止位点产生多个长非编码 RNA (lncRNA)。早期的细胞遗传学研究揭示了几种果蝇物种中 hsrω 的功能保守性。然而，三个物种的序列分析显示 ORFω、串联重复序列和其他区域的保守性较差，而分别发现 omega 内含子的 5' 和 3' 剪接点的 16 nt 和 60 nt 是超保守的。本生物信息学研究使用 D 中的剪接点标志物。melanogaster hsrω 在公开可用的 34 个果蝇物种基因组中鉴定了直向同源物。每个直向同源物携带一个短的 ORFω、omega 内含子的超保守剪接点、重复区域、位于 mir-4951 的保守 3'-末端和同线邻居。尽管重复序列的变异性很大，但在串联重复区域中可以看到多个拷贝的保守九聚体基序。有趣的是，只有不同物种的 omega 内含子序列显示出与该属的一般系统发育历史相匹配的进化关系。在其他已知昆虫基因组中的搜索没有揭示序列同源性，尽管在摇蚊属和 Ceratitis 属中提出了具有相似功能特性的基因座。在高度序列差异中，外显子的保守组织，