Analysis of 5'-end sequences of chimpanzee cDNAs.
We constructed full-length enriched cDNA libraries from chimpanzee brain, skin, and liver tissues by the oligo-capping method to establish a database of sequences of chimpanzee genes. 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. 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 (K(S)) and nonsynonymous (K(A)) divergences were estimated to be 1.33% and 0.28%, respectively.
Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan. sakate@prigen.org
Ryuichi
R
Sakate
Naoki
N
Osada
Munetomo
M
Hida
Sumio
S
Sugano
Ikuo
I
Hayasaka
Naoko
N
Shimohira
Shinsuke
S
Yanagi
Yumiko
Y
Suto
Katsuyuki
K
Hashimoto
Momoki
M
Hirai
D024506:5' Flanking Region / Q000235:genetics*; D000818:Animals; D001923:Brain Chemistry / Q000235:genetics; D017931:DNA Primers / Q000235:genetics; D018076:DNA, Complementary / Q000032:analysis*; D020224:Expressed Sequence Tags; D005260:Female; D006801:Humans; D008099:Liver / Q000737:chemistry / Q000378:metabolism; D008297:Male; D008969:Molecular Sequence Data; D009928:Organ Specificity / Q000235:genetics; D002679:Pan troglodytes / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012867:Skin / Q000737:chemistry / Q000378:metabolism
D017931:DNA Primers; D018076:DNA, Complementary