Target selection for Danio rerio functional genomics
Target selection for Danio rerio functional genomics
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DOI：
10.1002/gene.1045
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发表时间：
2001-07-01
期刊：
影响因子：
1.5
通讯作者：
Ellis, LBM
中科院分区：
文献类型：
--
作者：
Klee, EW;Ekker, SC;Ellis, LBM
使用真核生物之间的遗传同源性作为选择的斑马鱼（斑马鱼）序列的一个子集的基础上，具有高概率的编码分泌蛋白质的描述。获得了大部分基于表达序列标签（EST）的斑马鱼DNA和含有N-末端信号序列的果蝇基因组蛋白，并进行了比较。将非分泌数据集中的24个斑马鱼蛋白质序列与信号蛋白数据库中的2437个序列进行比较。五个非分泌序列与信号蛋白数据集中的序列相似。在与信号蛋白数据集中的序列匹配的五种非分泌型斑马鱼蛋白中，一种（热休克蛋白70，HSP-70）与其果蝇同源物具有强相似性，沿着整个共享序列长度。在斑马鱼和其他真核生物中，这种蛋白质是未知的分泌。果蝇蛋白可能不是分泌的，或者可能是第一个报告的分泌型HSP-70同源物。在10000个成员的斑马鱼数据集中，约有5%至6%在果蝇I型信号序列数据集中具有接近的同源物，因此具有被分泌的高概率。 非I型分泌的斑马鱼蛋白和果蝇中未发现的I型分泌的斑马鱼蛋白将增加估计值。另一方面，这种估计将减少果蝇信号序列数据集中的蛋白质，具有与多结构域斑马鱼蛋白质非常相似的单结构域，以及那些不分泌斑马鱼同源物的蛋白质。
The use of genetic homology among eukaryotes as a basis for selecting a subset of zebrafish (Danio rerio) sequences with high probability of encoding secreted proteins is described. Zebrafish DNA, most based on expressed sequence tags (ESTs), and proteins from the fruitflyDrosophila melanogastergenome containing N-terminal signal sequences were obtained and compared. The 24 zebrafish protein sequences in the non-secreted dataset were compared with the 2437 sequences in the signal protein database. Five non-secreted sequences are similar to sequences in the signal protein dataset. Of the five non-secreted zebrafish proteins that match sequences in the signal protein dataset, one (heat shock protein 70, Hsp-70) has strong similarity to its fruitfly homologue, along the entire length of the shared sequence. In zebrafish and other eukaryotes, this protein is not known to be secreted. The fruitfly protein may not be secreted or may be the first reported secreted Hsp-70 homologue. About 5 to 6% of the 10 000-member zebrafish dataset have close homologues in the fruitfly type I signal sequence data set, and thus have a high probability of being secreted. The estimate would be increased by non-type I secreted zebrafish proteins and type I secreted zebrafish proteins not found in fruitfly. On the other hand, this estimate would be reduced by proteins in the fruitfly signal sequence dataset with single domains very similar to ones in multidomain zebrafish proteins, and those whose zebrafish homologues are not secreted.