Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries.

Article Details

Citation

Otsuki T, Ota T, Nishikawa T, Hayashi K, Suzuki Y, Yamamoto J, Wakamatsu A, Kimura K, Sakamoto K, Hatano N, Kawai Y, Ishii S, Saito K, Kojima S, Sugiyama T, Ono T, Okano K, Yoshikawa Y, Aotsuka S, Sasaki N, Hattori A, Okumura K, Nagai K, Sugano S, Isogai T

Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries.

DNA Res. 2005;12(2):117-26.

PubMed ID
16303743 [ View in PubMed
]
Abstract

We have developed an in silico method of selection of human full-length cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. Fullness rates were increased to about 80% by combination of the oligo-capping method and ATGpr, software for prediction of translation start point and the coding potential. Then, using 5'-end single-pass sequences, cDNAs having the signal sequence were selected by PSORT ('signal sequence trap'). We also applied 'secretion or membrane protein-related keyword trap' based on the result of BLAST search against the SWISS-PROT database for the cDNAs which could not be selected by PSORT. Using the above procedures, 789 cDNAs were primarily selected and subjected to full-length sequencing, and 334 of these cDNAs were finally selected as novel. Most of the cDNAs (295 cDNAs: 88.3%) were predicted to encode secretion or membrane proteins. In particular, 165(80.5%) of the 205 cDNAs selected by PSORT were predicted to have signal sequences, while 70 (54.2%) of the 129 cDNAs selected by 'keyword trap' preserved the secretion or membrane protein-related keywords. Many important cDNAs were obtained, including transporters, receptors, and ligands, involved in significant cellular functions. Thus, an efficient method of selecting secretion or membrane protein-encoding cDNAs was developed by combining the above four procedures.

DrugBank Data that Cites this Article

Polypeptides
NameUniProt ID
Retinol dehydrogenase 13Q8NBN7Details
Cathepsin BP07858Details
Synaptic vesicle glycoprotein 2AQ7L0J3Details
CorticoliberinP06850Details
5'-nucleotidaseP21589Details
Tubulin beta-4A chainP04350Details
ADP-ribose pyrophosphatase, mitochondrialQ9BW91Details
Syndecan-2P34741Details
Choline transporter-like protein 2Q8IWA5Details
Prolyl 3-hydroxylase 1Q32P28Details
Fatty acid desaturase 2O95864Details
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrialO14521Details
Mitochondrial dicarboxylate carrierQ9UBX3Details
Thioredoxin domain-containing protein 12O95881Details
All-trans-retinol 13,14-reductaseQ6NUM9Details
Retinol dehydrogenase 11Q8TC12Details
Estradiol 17-beta-dehydrogenase 11Q8NBQ5Details
Transmembrane anterior posterior transformation protein 1 homologQ6NXT6Details
Pannexin-1Q96RD7Details
NADH-cytochrome b5 reductase 1Q9UHQ9Details
Carboxypeptidase QQ9Y646Details
Cytochrome P450 4F12Q9HCS2Details
Solute carrier family 2, facilitated glucose transporter member 6Q9UGQ3Details
Solute carrier family 2, facilitated glucose transporter member 11Q9BYW1Details
Elongation of very long chain fatty acids protein 5Q9NYP7Details
Solute carrier family 43 member 3Q8NBI5Details
Sodium-coupled neutral amino acid transporter 1Q9H2H9Details
Prostaglandin-H2 D-isomeraseP41222Details
Zinc transporter ZIP1Q9NY26Details
V-type proton ATPase subunit S1Q15904Details
UbiA prenyltransferase domain-containing protein 1Q9Y5Z9Details