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Analysis of 5'-end Sequences of Full-length cDNAs obtained from Chimpanzee Skin Tissues.

对从黑猩猩皮肤组织获得的全长 cDNA 的 5 端序列进行分析。

基本信息

批准号：
13554035
负责人：
HIRAI Momoki
金额：
$ 4.22万
依托单位：
The University of Tokyo
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (B)
财政年份：
2001
资助国家：
日本
起止时间：
2001 至 2003
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-13554035/
关键词：
Chimpanzee Full-length cDNA Sequencing Database Skin cDNA SNP 種特異性

项目摘要

We constructed full-length enriched cDNA libraries from chimpanzee skin and brain tissues by the oligo-capping method to establish a database of sequences of chimpanzee genes. The objective of this study was to precisely calculate sequence diversity between human and chimpanzee homologs. In addition, a comparative analysis of tissue-specific expressions of genes between humans and chimpanzees is expected to shed light on species specificity and evolution of humans. Randomly selected clones from the libraries were subjected to one-pass sequencing from their 5'-ends. As a result, we collected 6813 chimpanzee cDNA sequences longer than 400 bp. Homology search against human mRNA sequences (RefSeq mRNAs) revealed that our collection included sequences of 1652 putative chimpanzee genes. It was evident that the spectra of expressed genes in skin and brain tissues were different. For instance, in skin, keratin, vimentin and decorin genes were prominent. In order to calculate the sequence identity between human and chimpanzee homologs, we constructed 5'-end consensus sequences of 226 chimpanzee genes by aligning at least three sequences for individual genes. Sequence identity was estimated by comparing these consensus sequences and the corresponding sequences of their human homologs. The average sequence identity of the 5'-end cDNAs was 99.30%. Those of the 5'-UTRs and CDSs were 98.79% and 99.42%, respectively. The results confirmed that human and chimpanzee genes are highly conserved at the nucleotide level. As for amino acids, the average sequence identity was 99.44%. The average synonymous (KS) and nonsynonymous (KA) divergences were estimated to be 1.33% and 0.28%, respectively. Our collection of full-length cDNA clones and sequence data could be a valuable resource for postgenomic research.

为了建立黑猩猩基因序列数据库，我们采用寡核苷酸加帽法构建了黑猩猩皮肤和脑组织全长cDNA文库。本研究的目的是精确计算人类和黑猩猩同源物之间的序列多样性。此外，对人类和黑猩猩组织特异性基因表达的比较分析有望揭示人类的物种特异性和进化。从文库中随机选择的克隆从其5 '端进行一次测序。结果，我们收集了6813个大于400 bp的黑猩猩cDNA序列。对人类mRNA序列（RefSeq mRNA）的同源性搜索显示，我们的收集包括1652个假定的黑猩猩基因的序列。结果表明，皮肤和脑组织中基因表达谱存在差异。例如，在皮肤中，角蛋白、波形蛋白和核心蛋白聚糖基因是突出的。为了计算人类和黑猩猩同源物之间的序列同一性，我们通过对单个基因的至少三个序列进行比对，构建了226个黑猩猩基因的5 '端共有序列。通过比较这些共有序列及其人类同源物的相应序列来估计序列同一性。5 ′端cDNA序列的平均同源性为99.30%。5 '-UTR和CDS的阳性率分别为98.79%和99.42%。结果证实，人类和黑猩猩的基因在核苷酸水平上高度保守。氨基酸序列的平均同源性为99.44%。平均同义（KS）和非同义（KA）分歧估计分别为1.33%和0.28%。我们收集的全长cDNA克隆和序列数据可能是后基因组研究的宝贵资源。