Identification of mouse mslp2 gene from EST databases by repeated searching, comparison, and assembling.
The NPHS2 gene is expressed in podocytes and encodes the integral membrane protein called podocin, which is believed to play an important role in the renal function of glomerular filtration. Mutations in this gene can cause serious renal function disorders. In this study, we used data-mining techniques and bioinformatic tools to search for the mouse ortholog of the NPHS2-related gene. It might be valuable for future studies of renal diseases. We employed repeated cycles of searching, comparison, and assembling to extend the assembled EST sequences. The discovered gene sequence mslp2, an ortholog of the human SLP2 gene, was found to have a total length of 1253 bp with the amino acid coding region located in 32-1093 nt. It was further verified using the RT-PCR and RACE techniques to ensure its biological accuracy and then registered with the GenBank. When ClustalW was used for comparing the mslp2 and human SLP2 genes for similarities, the similarities were as high as 88% for nucleotide and 92% for amino acid sequences. In conclusion, we propose a method for rapid identification of the mouse ortholog gene from the human genome.
Chan
Wen-Ling
WL
Department of Computer Science, National Chung Hsing University, Taichung, Taiwan, ROC.
Chang
Jan-Gowth
JG
Chen
Yung-Fu
YF
Chan
Yung-Kuan
YK
Chu
Yen-Ping
YP
D000818:Animals; D001483:Base Sequence; D001798:Blood Proteins / Q000235:genetics*; D017931:DNA Primers; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins; D008565:Membrane Proteins / Q000235:genetics*; D051379:Mice; D021141:Nucleic Acid Amplification Techniques; D020133:Reverse Transcriptase Polymerase Chain Reaction; D020539:Sequence Analysis, Protein
D001798:Blood Proteins; D017931:DNA Primers; D047908:Intracellular Signaling Peptides and Proteins; D008565:Membrane Proteins; C407223:NPHS2 protein; C406287:STOML2 protein, human