Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones.

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Nakajima D, Okazaki N, Yamakawa H, Kikuno R, Ohara O, Nagase T

Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones.

DNA Res. 2002 Jun 30;9(3):99-106.

PubMed ID
12168954 [ View in PubMed
]
Abstract

We have accumulated information on protein-coding sequences of uncharacterized human genes, which are known as KIAA genes, through cDNA sequencing. For comprehensive functional analysis of the KIAA genes, it is necessary to prepare a set of cDNA clones which direct the synthesis of functional KIAA gene products. However, since the KIAA cDNAs were derived from long mRNAs (> 4 kb), it was not expected that all of them were full-length. Thus, as the first step toward preparing these clones, we evaluated the integrity of protein-coding sequences of KIAA cDNA clones through comparison with homologous protein entries in the public database. As a result, 1141 KIAA cDNAs had at least one homologous entry in the database, and 619 of them (54%) were found to be truncated at the 5' and/or 3' ends. In this study, 290 KIAA cDNA clones were tailored to be full-length or have considerably longer sequences than the original clones by isolating additional cDNA clones and/or connected parts of additional cDNAs or PCR products of the missing portion to the original cDNA clone. Consequently, 265, 8, and 17 predicted CDSs of KIAA cDNA clones were increased in the amino-, carboxy-, and both terminal sequences, respectively. In addition, 40 cDNA clones were modified to remove spurious interruption of protein-coding sequences. The total length of the resultant extensions at amino- and carboxy-terminals of KIAA gene products reached 97,000 and 7,216 amino acid residues, respectively, and various protein domains were found in these extended portions.

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Polypeptides
NameUniProt ID
Apoptotic protease-activating factor 1O14727Details
Voltage-dependent T-type calcium channel subunit alpha-1GO43497Details
Acetyl-coenzyme A synthetase 2-like, mitochondrialQ9NUB1Details
Beta-secretase 1P56817Details
Telomerase-binding protein EST1AQ86US8Details
Ribosome-binding protein 1Q9P2E9Details
Histone deacetylase 5Q9UQL6Details
Nuclear receptor coactivator 5Q9HCD5Details
MKL/myocardin-like protein 1Q969V6Details
Long-chain-fatty-acid--CoA ligase ACSBG1Q96GR2Details
Neurexin-1Q9ULB1Details
Protein O-GlcNAcaseO60502Details
HephaestinQ9BQS7Details
Calcium-dependent secretion activator 1Q9ULU8Details
Serine/threonine-protein kinase 38-likeQ9Y2H1Details
Serine/threonine-protein kinase tousled-like 1Q9UKI8Details
TRAF2 and NCK-interacting protein kinaseQ9UKE5Details
Serine/threonine-protein kinase ULK1O75385Details
Calcium/calmodulin-dependent protein kinase kinase 2Q96RR4Details
Serine/threonine-protein kinase SIK3Q9Y2K2Details
Serine/threonine-protein kinase SIK2Q9H0K1Details
SNF-related serine/threonine-protein kinaseQ9NRH2Details
Solute carrier family 23 member 2Q9UGH3Details
Sodium-coupled neutral amino acid transporter 2Q96QD8Details
Cell surface hyaluronidaseQ9UHN6Details
Adenylate cyclase type 6O43306Details
Adenylate cyclase type 9O60503Details