Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.
Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.
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在十种物种中，基因组在计算机鉴定和分析中的二氧化硅自然反义转录本（顺式核）中。
DOI：
10.1093/nar/gkl473
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发表时间：
2006
影响因子：
14.9
通讯作者：
Wei, Liping
中科院分区：
文献类型：
--
作者：
Zhang, Yong;Liu, X. Shirley;Liu, Qing-Rong;Wei, Liping
我们开发了一个快速，综合的管道，以确定顺式天然反义转录本（顺式NAT）在基因组规模。管道将UniGene中的mRNA和EST映射到GoldenPath中的基因组序列，以找到重叠的转录本，并结合编码序列、poly（A）信号、poly（A）尾和剪接位点的信息来推断转录方向。我们在10个真核生物物种中鉴定了顺式NAT，其中包括人类3915个SA对中的7830个候选SA基因。SA基因的丰度在蠕虫中非常低，似乎不是由操纵子的流行引起的。数以百计的SA对在不同的物种中是保守的，甚至保持相同的重叠模式。收敛SA类是普遍存在于苍蝇，蠕虫和海鞘，但不是在人类或小鼠如前所述。SA基因在人类和小鼠的印迹基因中所占的百分比为24- 47%，介于前两个报告之间。在人类和小鼠的X染色体上SA基因明显不足，但在苍蝇或蠕虫中没有，这支持哺乳动物的X失活是一个可能的原因。SA基因在催化活性和基本代谢功能中占优势。所有候选cis-NAT均可从下载。
We developed a fast, integrative pipeline to identify cis natural antisense transcripts (cis-NATs) at genome scale. The pipeline mapped mRNAs and ESTs in UniGene to genome sequences in GoldenPath to find overlapping transcripts and combining information from coding sequence, poly(A) signal, poly(A) tail and splicing sites to deduce transcription orientation. We identified cis-NATs in 10 eukaryotic species, including 7830 candidate sense–antisense (SA) genes in 3915 SA pairs in human. The abundance of SA genes is remarkably low in worm and does not seem to be caused by the prevalence of operons. Hundreds of SA pairs are conserved across different species, even maintaining the same overlapping patterns. The convergent SA class is prevalent in fly, worm and sea squirt, but not in human or mouse as reported previously. The percentage of SA genes among imprinted genes in human and mouse is 24–47%, a range between the two previous reports. There is significant shortage of SA genes on Chromosome X in human and mouse but not in fly or worm, supporting X-inactivation in mammals as a possible cause. SA genes are over-represented in the catalytic activities and basic metabolism functions. All candidate cis-NATs can be downloaded from .
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影响因子：
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作者：
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通讯作者：
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