A survey of genes expressed in mouse embryonal carcinoma F9 cells: characterization of expressed sequence tags matching no known genes.
We prepared 2,132 expressed sequence tags (ESTs) from undifferentiated mouse embryonal carcinoma F9 cells and found that 1,416 match known gene and/or protein sequences [Nishiguchi et al. (1996) J. Biochem. 119, 749-767]. To obtain information on the functions of the remaining 716 unidentified ESTs and to develop a system for characterizing ESTs matching no known genes, we analyzed their sequences by (i) repeated database searches, using the BLASTN, BLASTX, TBLASTX, and FASTA programs, (ii) using computer programs developed or modified for this work, such as the WFASTA, ORFTRNS, and MFASTA programs, together with the DBPROSITE and GRAIL programs, and (iii) examining the expression patterns of the corresponding mRNAs in F9 cells and several organs of adult mice, using the digoxigenin-labeled dot-blot method. We found that 216 of the 716 ESTs match known gene and/or protein sequences, and 307 show significant similarities to these sequences, with a Poisson p-value < 0.01. The strategy and usefulness of such analysis for characterizing unidentified ESTs are discussed.
Nomura
M
M
Department of Medical Genetics, Research Institute for Microbial Diseases, Osaka University.
Nishiguchi
S
S
Motaleb
M A
MA
Takihara
Y
Y
Takagi
T
T
Yasunaga
T
T
Shimada
K
K
D000818:Animals; D015152:Blotting, Northern; D018236:Carcinoma, Embryonal / Q000188:drug therapy / Q000235:genetics*; D002454:Cell Differentiation / Q000187:drug effects / Q000235:genetics; D016208:Databases, Factual; D018507:Gene Expression Regulation, Developmental; D051379:Mice; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D009928:Organ Specificity; D012333:RNA, Messenger; D017386:Sequence Homology, Amino Acid; D016324:Sequence Tagged Sites; D012984:Software; D014018:Tissue Distribution; D014212:Tretinoin / Q000494:pharmacology; D014407:Tumor Cells, Cultured
D012333:RNA, Messenger; D014212:Tretinoin