The full-ORF clone resource of the German cDNA Consortium.

Article Details

Citation

Bechtel S, Rosenfelder H, Duda A, Schmidt CP, Ernst U, Wellenreuther R, Mehrle A, Schuster C, Bahr A, Blocker H, Heubner D, Hoerlein A, Michel G, Wedler H, Kohrer K, Ottenwalder B, Poustka A, Wiemann S, Schupp I

The full-ORF clone resource of the German cDNA Consortium.

BMC Genomics. 2007 Oct 31;8:399.

PubMed ID
17974005 [ View in PubMed
]
Abstract

BACKGROUND: With the completion of the human genome sequence the functional analysis and characterization of the encoded proteins has become the next urging challenge in the post-genome era. The lack of comprehensive ORFeome resources has thus far hampered systematic applications by protein gain-of-function analysis. Gene and ORF coverage with full-length ORF clones thus needs to be extended. In combination with a unique and versatile cloning system, these will provide the tools for genome-wide systematic functional analyses, to achieve a deeper insight into complex biological processes. RESULTS: Here we describe the generation of a full-ORF clone resource of human genes applying the Gateway cloning technology (Invitrogen). A pipeline for efficient cloning and sequencing was developed and a sample tracking database was implemented to streamline the clone production process targeting more than 2,200 different ORFs. In addition, a robust cloning strategy was established, permitting the simultaneous generation of two clone variants that contain a particular ORF with as well as without a stop codon by the implementation of only one additional working step into the cloning procedure. Up to 92 % of the targeted ORFs were successfully amplified by PCR and more than 93 % of the amplicons successfully cloned. CONCLUSION: The German cDNA Consortium ORFeome resource currently consists of more than 3,800 sequence-verified entry clones representing ORFs, cloned with and without stop codon, for about 1,700 different gene loci. 177 splice variants were cloned representing 121 of these genes. The entry clones have been used to generate over 5,000 different expression constructs, providing the basis for functional profiling applications. As a member of the recently formed international ORFeome collaboration we substantially contribute to generating and providing a whole genome human ORFeome collection in a unique cloning system that is made freely available in the community.

DrugBank Data that Cites this Article

Polypeptides
NameUniProt ID
NAD(P) transhydrogenase, mitochondrialQ13423Details
Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrialP50213Details
3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 2P26439Details
Ferritin light chainP02792Details
S-adenosylmethionine decarboxylase proenzymeP17707Details
Ketimine reductase mu-crystallinQ14894Details
Adenine phosphoribosyltransferaseP07741Details
Estrogen receptorP03372Details
Solute carrier family 12 member 6Q9UHW9Details
Bifunctional glutamate/proline--tRNA ligaseP07814Details
Solute carrier family 12 member 7Q9Y666Details
Sodium-coupled neutral amino acid transporter 3Q99624Details
GDH/6PGL endoplasmic bifunctional proteinO95479Details
Ornithine aminotransferase, mitochondrialP04181Details
Abelson tyrosine-protein kinase 2P42684Details
Leucine carboxyl methyltransferase 1Q9UIC8Details
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5Q16718Details
Isoleucine--tRNA ligase, cytoplasmicP41252Details
Retinal dehydrogenase 2O94788Details
Branched-chain-amino-acid aminotransferase, cytosolicP54687Details
Serum albuminP02768Details
Proton-coupled amino acid transporter 1Q7Z2H8Details
Isocitrate dehydrogenase [NAD] subunit beta, mitochondrialO43837Details
Cationic amino acid transporter 2P52569Details
Spermine oxidaseQ9NWM0Details
Short/branched chain specific acyl-CoA dehydrogenase, mitochondrialP45954Details
Squalene monooxygenaseQ14534Details
Solute carrier family 13 member 3Q8WWT9Details
Monocarboxylate transporter 1P53985Details
Phosphatidylserine decarboxylase proenzymeQ9UG56Details
Acid-sensing ion channel 2Q16515Details
Cysteine--tRNA ligase, cytoplasmicP49589Details
Aspartate--tRNA ligase, cytoplasmicP14868Details
N(G),N(G)-dimethylarginine dimethylaminohydrolase 1O94760Details
Glucocorticoid receptorP04150Details
Glutathione S-transferase A4O15217Details
Glutathione S-transferase omega-1P78417Details
Fatty acid desaturase 1O60427Details
CalpastatinP20810Details
Alpha-2-macroglobulinP01023Details
Cytosolic 10-formyltetrahydrofolate dehydrogenaseO75891Details
Angiotensin-converting enzyme 2Q9BYF1Details
Synaptic vesicle glycoprotein 2AQ7L0J3Details
Cytochrome cP99999Details
Solute carrier organic anion transporter family member 2B1O94956Details
ElastinP15502Details
Proton-coupled folate transporterQ96NT5Details
85/88 kDa calcium-independent phospholipase A2O60733Details
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2P59768Details
Inactive phospholipase C-like protein 1Q15111Details
Nuclear factor NF-kappa-B p105 subunitP19838Details
CD44 antigenP16070Details
Annexin A2P07355Details
FibronectinP02751Details
Quinone oxidoreductaseQ08257Details
Transforming protein RhoAP61586Details
RhodopsinP08100Details
Isocitrate dehydrogenase [NADP] cytoplasmicO75874Details
Dual adapter for phosphotyrosine and 3-phosphotyrosine and 3-phosphoinositideQ9UN19Details
Cathepsin FQ9UBX1Details
Leukotriene A-4 hydrolaseP09960Details
Death-associated protein kinase 1P53355Details
Fatty acid-binding protein, brainO15540Details
Serpin B5P36952Details
Estrogen-related receptor gammaP62508Details
Complement C1r subcomponentP00736Details
Plasma serine protease inhibitorP05154Details
Multiple coagulation factor deficiency protein 2Q8NI22Details
Synaptotagmin-like protein 4Q96C24Details
Neuropilin-1O14786Details
Cathepsin L1P07711Details
Vesicle-associated membrane protein 1P23763Details
Serpin B6P35237Details
SPARCP09486Details
Kynurenine--oxoglutarate transaminase 3Q6YP21Details
Acidic amino acid decarboxylase GADL1Q6ZQY3Details
Molybdenum cofactor sulfuraseQ96EN8Details
O-phosphoseryl-tRNA(Sec) selenium transferaseQ9HD40Details
Methylmalonic aciduria and homocystinuria type C proteinQ9Y4U1Details
Choline transporter-like protein 4Q53GD3Details
Choline transporter-like protein 2Q8IWA5Details
Choline/ethanolaminephosphotransferase 1Q9Y6K0Details
2-oxoglutarate and iron-dependent oxygenase domain-containing protein 2Q6N063Details
Egl nine homolog 2Q96KS0Details
Egl nine homolog 1Q9GZT9Details
Transmembrane prolyl 4-hydroxylaseQ9NXG6Details
Multifunctional protein ADE2P22234Details
Glutamine synthetaseP15104Details
Fatty acid desaturase 2O95864Details
Beta-1,4-galactosyltransferase 4O60513Details
Beta-1,4-galactosyltransferase 2O60909Details
5-oxoprolinaseO14841Details
Probable glutamate--tRNA ligase, mitochondrialQ5JPH6Details
Phosphatidylserine synthase 2Q9BVG9Details
Short-chain dehydrogenase/reductase 3O75911Details
Vitamin K epoxide reductase complex subunit 1-like protein 1Q8N0U8Details
Probable proline--tRNA ligase, mitochondrialQ7L3T8Details
Proteasome subunit beta type-5P28074Details
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alphaP49354Details
E3 ubiquitin-protein ligase UBR4Q5T4S7Details
Telomerase-binding protein EST1AQ86US8Details
Hypoxia-inducible factor 1-alpha inhibitorQ9NWT6Details
Kinesin-like protein KIF1AQ12756Details
Hepatocyte nuclear factor 4-gammaQ14541Details
Lethal(3)malignant brain tumor-like protein 1Q9Y468Details
Anthrax toxin receptor 2P58335Details
NAD-dependent protein deacylase sirtuin-5, mitochondrialQ9NXA8Details
High mobility group protein B1P09429Details
Tumor necrosis factor receptor superfamily member 10BO14763Details
Ribosome-binding protein 1Q9P2E9Details
Microtubule-associated protein 4P27816Details
SLAM family member 7Q9NQ25Details
Bcl-2-like protein 1Q07817Details
Histone deacetylase 7Q8WUI4Details
Histone deacetylase 10Q969S8Details
Nuclear receptor ROR-betaQ92753Details
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gammaP18545Details
Prostaglandin reductase 2Q8N8N7Details
Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1AP54750Details
Integrin beta-1P05556Details
NischarinQ9Y2I1Details
Gamma-aminobutyric acid receptor subunit gamma-1Q8N1C3Details
Ribonucleoside-diphosphate reductase subunit M2 BQ7LG56Details
Gastric triacylglycerol lipaseP07098Details
High affinity copper uptake protein 1O15431Details
Multidrug resistance-associated protein 7Q5T3U5Details
Solute carrier organic anion transporter family member 1C1Q9NYB5Details
High affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8BO95263Details
Receptor-type tyrosine-protein phosphatase betaP23467Details
60S ribosomal protein L19P84098Details
Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrialQ16134Details
Myosin-14Q7Z406Details
GlycodelinP09466Details
Dihydrofolate reductase, mitochondrialQ86XF0Details
Poly [ADP-ribose] polymerase 3Q9Y6F1Details
Elongation factor Tu GTP-binding domain-containing protein 1Q7Z2Z2Details
Arylacetamide deacetylase-like 2Q6P093Details
Peroxisomal acyl-coenzyme A oxidase 1Q15067Details
MKL/myocardin-like protein 1Q969V6Details
Protein spire homolog 2Q8WWL2Details
Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoformQ08209Details
Actin-related protein 2P61160Details
Casein kinase I isoform gamma-1Q9HCP0Details
Trafficking protein particle complex subunit 6BQ86SZ2Details
AfadinP55196Details
Type II inositol 1,4,5-trisphosphate 5-phosphataseP32019Details
tRNA-splicing ligase RtcB homologQ9Y3I0Details
Citrate synthase, mitochondrialO75390Details
Uridine 5'-monophosphate synthaseP11172Details
cAMP-dependent protein kinase catalytic subunit betaP22694Details
Ras-related protein Rab-8BQ92930Details
Inositol-3-phosphate synthase 1Q9NPH2Details
FumarylacetoacetaseP16930Details
ADP-ribosylation factor-like protein 1P40616Details
NAD-dependent protein deacetylase sirtuin-3, mitochondrialQ9NTG7Details
T-complex protein 1 subunit gammaP49368Details
N-acylneuraminate cytidylyltransferaseQ8NFW8Details
Phosphoserine phosphataseP78330Details
Pyrroline-5-carboxylate reductase 3Q53H96Details
Serine/threonine-protein kinase TAO2Q9UL54Details
Polycomb protein SCMH1Q96GD3Details
Carbamoyl-phosphate synthase [ammonia], mitochondrialP31327Details
Sodium bicarbonate cotransporter 3Q9Y6M7Details
Electroneutral sodium bicarbonate exchanger 1Q2Y0W8Details
Sodium-driven chloride bicarbonate exchangerQ6U841Details
Cocaine esteraseO00748Details
Cytochrome P450 4F12Q9HCS2Details
Multidrug and toxin extrusion protein 2Q86VL8Details
Protein cereblonQ96SW2Details
Serine/threonine-protein kinase Nek11Q8NG66Details
Ephrin type-A receptor 5P54756Details
Alpha-enolaseP06733Details
Protocadherin-19Q8TAB3Details
Hephaestin-like protein 1Q6MZM0Details
Endonuclease 8-like 2Q969S2Details
Histone deacetylase 11Q96DB2Details
Calcium-dependent secretion activator 1Q9ULU8Details
Calcium-dependent secretion activator 2Q86UW7Details
Diacylglycerol O-acyltransferase 2Q96PD7Details
Heterogeneous nuclear ribonucleoprotein H3P31942Details
Protein RIC-3Q7Z5B4Details
Tubulin monoglycylase TTLL3Q9Y4R7Details
Splicing factor 3B subunit 3Q15393Details
Tropomyosin alpha-1 chainP09493Details
ClusterinP10909Details
Heterochromatin protein 1-binding protein 3Q5SSJ5Details
N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase DQ6IQ20Details
Myosin-9P35579Details
Voltage-dependent calcium channel subunit alpha-2/delta-4Q7Z3S7Details
Atypical kinase COQ8A, mitochondrialQ8NI60Details
Serine/threonine-protein kinase 33Q9BYT3Details
Serine/threonine-protein kinase 36Q9NRP7Details
Serine/threonine-protein kinase TAO3Q9H2K8Details
Serine/threonine-protein kinase TNNI3KQ59H18Details
Serine/threonine-protein kinase ULK3Q6PHR2Details
BMP-2-inducible protein kinaseQ9NSY1Details
Calcium/calmodulin-dependent protein kinase kinase 2Q96RR4Details
Serine/threonine-protein kinase DCLK2Q8N568Details
Eukaryotic translation initiation factor 2-alpha kinase 1Q9BQI3Details
eIF-2-alpha kinase GCN2Q9P2K8Details
Ephrin type-A receptor 6Q9UF33Details
Leucine-rich repeat serine/threonine-protein kinase 2Q5S007Details
Mitogen-activated protein kinase kinase kinase 3Q99759Details
Mitogen-activated protein kinase kinase kinase kinase 4O95819Details
MAP kinase-activated protein kinase 5Q8IW41Details
CLIP-associating protein 1Q7Z460Details
Megakaryocyte-associated tyrosine-protein kinaseP42679Details
Serine/threonine-protein kinase Nek1Q96PY6Details
Serine/threonine-protein kinase PAK 4O96013Details
Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinaseQ99640Details
Serine/threonine-protein kinase RIO1Q9BRS2Details
SNF-related serine/threonine-protein kinaseQ9NRH2Details
Serine/threonine-protein kinase 10O94804Details
Exportin-1O14980Details
Mitogen-activated protein kinase 6Q16659Details
Solute carrier family 43 member 3Q8NBI5Details
Lysophosphatidic acid receptor 6P43657Details
Solute carrier family 41 member 1Q8IVJ1Details
Y+L amino acid transporter 2Q92536Details
Receptor for retinol uptake STRA6Q9BX79Details
Zinc transporter ZIP10Q9ULF5Details
Zinc transporter 7Q8NEW0Details
Zinc transporter 8Q8IWU4Details
Zinc transporter 5Q8TAD4Details
Zinc transporter 10Q6XR72Details
Zinc transporter ZIP13Q96H72Details
Zinc transporter 6Q6NXT4Details
Diacylglycerol kinase etaQ86XP1Details
V-type proton ATPase subunit e 2Q8NHE4Details
V-type proton ATPase 116 kDa subunit a isoform 1Q93050Details
Plasma membrane calcium-transporting ATPase 4P23634Details
Calcium-transporting ATPase type 2C member 2O75185Details
PI-PLC X domain-containing protein 3Q63HM9Details