Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs.
Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs.
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Sno/scaRNAbase：小核仁 RNA 和 cajal 体特异性 RNA 的精选数据库
DOI：
10.1093/nar/gkl873
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发表时间：
2007-01
影响因子：
14.9
通讯作者：
Wu W
中科院分区：
文献类型：
--
作者：
Xie J;Zhang M;Zhou T;Hua X;Tang L;Wu W
小核仁RNA（snoRNA）和卡哈尔体特异性RNA（scaRNA）分别因其在核仁和卡哈尔体（存在于核质中的保守亚核细胞器）中的亚细胞定位而命名。已发现它们在rRNA、tRNA、snRNA甚至mRNA修饰和加工中发挥重要作用。所有snoRNA根据其独特的序列和二级结构特征分为两类，box C/D snoRNA和box H/ACA snoRNA。Box C/D snoRNA和box H/ACA snoRNA主要分别在2′-O-核糖甲基化和假尿嘧啶扩张中起作用。ScaRNA具有盒C/D snoRNA和盒H/ACA snoRNA序列基序特征，但引导由RNA聚合酶II转录的snRNA修饰。在这里，我们提出了一个基于Web的sno/scaRNA数据库，称为sno/scaRNAbase，以促进sno/scaRNA的研究方面提供了一个更全面的知识库。sno/scaRNAbase首次涵盖了来自85种生物的1979条记录，不仅致力于填补现有生物特异性sno/scaRNA数据库之间的空白，这些数据库专注于不同的sno/scaRNA方面，而且还为sno/scaRNA科学家提供了采用统一命名法的机会。通过系统的文献整理和注释工作，sno/scaRNAbase为重要的sno/scaRNA特征提供了一个易于使用的门户，例如序列基序、可能的功能、同源物、二级结构、基因组学组织、sno/scaRNA基因的染色体位置等。除了精确和直接的搜索外，近似搜索使数据库搜索更加灵活。实施BLAST搜索引擎以使得能够针对所有sno/scaRNAbase序列对查询序列进行blast。因此，我们的sno/scaRNAbase为sno/scaRNA研究提供了一个更加统一和友好的平台。该数据库可在以下网址免费获取。
Small nucleolar RNAs (snoRNAs) and Cajal body-specific RNAs (scaRNAs) are named for their subcellular localization within nucleoli and Cajal bodies (conserved subnuclear organelles present in the nucleoplasm), respectively. They have been found to play important roles in rRNA, tRNA, snRNAs, and even mRNA modification and processing. All snoRNAs fall in two categories, box C/D snoRNAs and box H/ACA snoRNAs, according to their distinct sequence and secondary structure features. Box C/D snoRNAs and box H/ACA snoRNAs mainly function in guiding 2′-O-ribose methylation and pseudouridilation, respectively. ScaRNAs possess both box C/D snoRNA and box H/ACA snoRNA sequence motif features, but guide snRNA modifications that are transcribed by RNA polymerase II. Here we present a Web-based sno/scaRNA database, called sno/scaRNAbase, to facilitate the sno/scaRNA research in terms of providing a more comprehensive knowledge base. Covering 1979 records derived from 85 organisms for the first time, sno/scaRNAbase is not only dedicated to filling gaps between existing organism-specific sno/scaRNA databases that are focused on different sno/scaRNA aspects, but also provides sno/scaRNA scientists with an opportunity to adopt a unified nomenclature for sno/scaRNAs. Derived from a systematic literature curation and annotation effort, the sno/scaRNAbase provides an easy-to-use gateway to important sno/scaRNA features such as sequence motifs, possible functions, homologues, secondary structures, genomics organization, sno/scaRNA gene's chromosome location, and more. Approximate searches, in addition to accurate and straightforward searches, make the database search more flexible. A BLAST search engine is implemented to enable blast of query sequences against all sno/scaRNAbase sequences. Thus our sno/scaRNAbase serves as a more uniform and friendly platform for sno/scaRNA research. The database is free available at .
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影响因子：
11.4
作者：
Dheur, S;Vo, LTA;Minvielle-Sebastia, L
通讯作者：
Minvielle-Sebastia, L
影响因子：
1.8
作者：
HOFACKER, IL;FONTANA, W;SCHUSTER, P
通讯作者：
SCHUSTER, P
影响因子：
16
作者：
Grandi, P;Rybin, V;Hurt, E
通讯作者：
Hurt, E
影响因子：
10.5
作者：
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通讯作者：
Kiss, T
影响因子：
64.8
作者：
Cavaille, J;Nicoloso, M;Bachellerie, JP
通讯作者：
Bachellerie, JP