The full-ORF clone resource of the German cDNA Consortium.
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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
Name UniProt ID NAD(P) transhydrogenase, mitochondrial Q13423 Details Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial P50213 Details 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 2 P26439 Details Ferritin light chain P02792 Details S-adenosylmethionine decarboxylase proenzyme P17707 Details Ketimine reductase mu-crystallin Q14894 Details Adenine phosphoribosyltransferase P07741 Details Estrogen receptor P03372 Details Solute carrier family 12 member 6 Q9UHW9 Details Bifunctional glutamate/proline--tRNA ligase P07814 Details Solute carrier family 12 member 7 Q9Y666 Details Sodium-coupled neutral amino acid transporter 3 Q99624 Details GDH/6PGL endoplasmic bifunctional protein O95479 Details Ornithine aminotransferase, mitochondrial P04181 Details Abelson tyrosine-protein kinase 2 P42684 Details Leucine carboxyl methyltransferase 1 Q9UIC8 Details NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 Q16718 Details Isoleucine--tRNA ligase, cytoplasmic P41252 Details Retinal dehydrogenase 2 O94788 Details Branched-chain-amino-acid aminotransferase, cytosolic P54687 Details Serum albumin P02768 Details Proton-coupled amino acid transporter 1 Q7Z2H8 Details Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial O43837 Details Cationic amino acid transporter 2 P52569 Details Spermine oxidase Q9NWM0 Details Short/branched chain specific acyl-CoA dehydrogenase, mitochondrial P45954 Details Squalene monooxygenase Q14534 Details Solute carrier family 13 member 3 Q8WWT9 Details Monocarboxylate transporter 1 P53985 Details Phosphatidylserine decarboxylase proenzyme Q9UG56 Details Acid-sensing ion channel 2 Q16515 Details Cysteine--tRNA ligase, cytoplasmic P49589 Details Aspartate--tRNA ligase, cytoplasmic P14868 Details N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 O94760 Details Glucocorticoid receptor P04150 Details Glutathione S-transferase A4 O15217 Details Glutathione S-transferase omega-1 P78417 Details Fatty acid desaturase 1 O60427 Details Calpastatin P20810 Details Alpha-2-macroglobulin P01023 Details Cytosolic 10-formyltetrahydrofolate dehydrogenase O75891 Details Angiotensin-converting enzyme 2 Q9BYF1 Details Synaptic vesicle glycoprotein 2A Q7L0J3 Details Cytochrome c P99999 Details Solute carrier organic anion transporter family member 2B1 O94956 Details Elastin P15502 Details Proton-coupled folate transporter Q96NT5 Details 85/88 kDa calcium-independent phospholipase A2 O60733 Details Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 P59768 Details Inactive phospholipase C-like protein 1 Q15111 Details Nuclear factor NF-kappa-B p105 subunit P19838 Details CD44 antigen P16070 Details Annexin A2 P07355 Details Fibronectin P02751 Details Quinone oxidoreductase Q08257 Details Transforming protein RhoA P61586 Details Rhodopsin P08100 Details Isocitrate dehydrogenase [NADP] cytoplasmic O75874 Details Dual adapter for phosphotyrosine and 3-phosphotyrosine and 3-phosphoinositide Q9UN19 Details Cathepsin F Q9UBX1 Details Leukotriene A-4 hydrolase P09960 Details Death-associated protein kinase 1 P53355 Details Fatty acid-binding protein, brain O15540 Details Serpin B5 P36952 Details Estrogen-related receptor gamma P62508 Details Complement C1r subcomponent P00736 Details Plasma serine protease inhibitor P05154 Details Multiple coagulation factor deficiency protein 2 Q8NI22 Details Synaptotagmin-like protein 4 Q96C24 Details Neuropilin-1 O14786 Details Cathepsin L1 P07711 Details Vesicle-associated membrane protein 1 P23763 Details Serpin B6 P35237 Details SPARC P09486 Details Kynurenine--oxoglutarate transaminase 3 Q6YP21 Details Acidic amino acid decarboxylase GADL1 Q6ZQY3 Details Molybdenum cofactor sulfurase Q96EN8 Details O-phosphoseryl-tRNA(Sec) selenium transferase Q9HD40 Details Methylmalonic aciduria and homocystinuria type C protein Q9Y4U1 Details Choline transporter-like protein 4 Q53GD3 Details Choline transporter-like protein 2 Q8IWA5 Details Choline/ethanolaminephosphotransferase 1 Q9Y6K0 Details 2-oxoglutarate and iron-dependent oxygenase domain-containing protein 2 Q6N063 Details Egl nine homolog 2 Q96KS0 Details Egl nine homolog 1 Q9GZT9 Details Transmembrane prolyl 4-hydroxylase Q9NXG6 Details Multifunctional protein ADE2 P22234 Details Glutamine synthetase P15104 Details Fatty acid desaturase 2 O95864 Details Beta-1,4-galactosyltransferase 4 O60513 Details Beta-1,4-galactosyltransferase 2 O60909 Details 5-oxoprolinase O14841 Details Probable glutamate--tRNA ligase, mitochondrial Q5JPH6 Details Phosphatidylserine synthase 2 Q9BVG9 Details Short-chain dehydrogenase/reductase 3 O75911 Details Vitamin K epoxide reductase complex subunit 1-like protein 1 Q8N0U8 Details Probable proline--tRNA ligase, mitochondrial Q7L3T8 Details Proteasome subunit beta type-5 P28074 Details Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha P49354 Details E3 ubiquitin-protein ligase UBR4 Q5T4S7 Details Telomerase-binding protein EST1A Q86US8 Details Hypoxia-inducible factor 1-alpha inhibitor Q9NWT6 Details Kinesin-like protein KIF1A Q12756 Details Hepatocyte nuclear factor 4-gamma Q14541 Details Lethal(3)malignant brain tumor-like protein 1 Q9Y468 Details Anthrax toxin receptor 2 P58335 Details NAD-dependent protein deacylase sirtuin-5, mitochondrial Q9NXA8 Details High mobility group protein B1 P09429 Details Tumor necrosis factor receptor superfamily member 10B O14763 Details Ribosome-binding protein 1 Q9P2E9 Details Microtubule-associated protein 4 P27816 Details SLAM family member 7 Q9NQ25 Details Bcl-2-like protein 1 Q07817 Details Histone deacetylase 7 Q8WUI4 Details Histone deacetylase 10 Q969S8 Details Nuclear receptor ROR-beta Q92753 Details Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma P18545 Details Prostaglandin reductase 2 Q8N8N7 Details Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1A P54750 Details Integrin beta-1 P05556 Details Nischarin Q9Y2I1 Details Gamma-aminobutyric acid receptor subunit gamma-1 Q8N1C3 Details Ribonucleoside-diphosphate reductase subunit M2 B Q7LG56 Details Gastric triacylglycerol lipase P07098 Details High affinity copper uptake protein 1 O15431 Details Multidrug resistance-associated protein 7 Q5T3U5 Details Solute carrier organic anion transporter family member 1C1 Q9NYB5 Details High affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8B O95263 Details Receptor-type tyrosine-protein phosphatase beta P23467 Details 60S ribosomal protein L19 P84098 Details Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial Q16134 Details Myosin-14 Q7Z406 Details Glycodelin P09466 Details Dihydrofolate reductase, mitochondrial Q86XF0 Details Poly [ADP-ribose] polymerase 3 Q9Y6F1 Details Elongation factor Tu GTP-binding domain-containing protein 1 Q7Z2Z2 Details Arylacetamide deacetylase-like 2 Q6P093 Details Peroxisomal acyl-coenzyme A oxidase 1 Q15067 Details MKL/myocardin-like protein 1 Q969V6 Details Protein spire homolog 2 Q8WWL2 Details Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform Q08209 Details Actin-related protein 2 P61160 Details Casein kinase I isoform gamma-1 Q9HCP0 Details Trafficking protein particle complex subunit 6B Q86SZ2 Details Afadin P55196 Details Type II inositol 1,4,5-trisphosphate 5-phosphatase P32019 Details tRNA-splicing ligase RtcB homolog Q9Y3I0 Details Citrate synthase, mitochondrial O75390 Details Uridine 5'-monophosphate synthase P11172 Details cAMP-dependent protein kinase catalytic subunit beta P22694 Details Ras-related protein Rab-8B Q92930 Details Inositol-3-phosphate synthase 1 Q9NPH2 Details Fumarylacetoacetase P16930 Details ADP-ribosylation factor-like protein 1 P40616 Details NAD-dependent protein deacetylase sirtuin-3, mitochondrial Q9NTG7 Details T-complex protein 1 subunit gamma P49368 Details N-acylneuraminate cytidylyltransferase Q8NFW8 Details Phosphoserine phosphatase P78330 Details Pyrroline-5-carboxylate reductase 3 Q53H96 Details Serine/threonine-protein kinase TAO2 Q9UL54 Details Polycomb protein SCMH1 Q96GD3 Details Carbamoyl-phosphate synthase [ammonia], mitochondrial P31327 Details Sodium bicarbonate cotransporter 3 Q9Y6M7 Details Electroneutral sodium bicarbonate exchanger 1 Q2Y0W8 Details Sodium-driven chloride bicarbonate exchanger Q6U841 Details Cocaine esterase O00748 Details Cytochrome P450 4F12 Q9HCS2 Details Multidrug and toxin extrusion protein 2 Q86VL8 Details Protein cereblon Q96SW2 Details Serine/threonine-protein kinase Nek11 Q8NG66 Details Ephrin type-A receptor 5 P54756 Details Alpha-enolase P06733 Details Protocadherin-19 Q8TAB3 Details Hephaestin-like protein 1 Q6MZM0 Details Endonuclease 8-like 2 Q969S2 Details Histone deacetylase 11 Q96DB2 Details Calcium-dependent secretion activator 1 Q9ULU8 Details Calcium-dependent secretion activator 2 Q86UW7 Details Diacylglycerol O-acyltransferase 2 Q96PD7 Details Heterogeneous nuclear ribonucleoprotein H3 P31942 Details Protein RIC-3 Q7Z5B4 Details Tubulin monoglycylase TTLL3 Q9Y4R7 Details Splicing factor 3B subunit 3 Q15393 Details Tropomyosin alpha-1 chain P09493 Details Clusterin P10909 Details Heterochromatin protein 1-binding protein 3 Q5SSJ5 Details N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D Q6IQ20 Details Myosin-9 P35579 Details Voltage-dependent calcium channel subunit alpha-2/delta-4 Q7Z3S7 Details Atypical kinase COQ8A, mitochondrial Q8NI60 Details Serine/threonine-protein kinase 33 Q9BYT3 Details Serine/threonine-protein kinase 36 Q9NRP7 Details Serine/threonine-protein kinase TAO3 Q9H2K8 Details Serine/threonine-protein kinase TNNI3K Q59H18 Details Serine/threonine-protein kinase ULK3 Q6PHR2 Details BMP-2-inducible protein kinase Q9NSY1 Details Calcium/calmodulin-dependent protein kinase kinase 2 Q96RR4 Details Serine/threonine-protein kinase DCLK2 Q8N568 Details Eukaryotic translation initiation factor 2-alpha kinase 1 Q9BQI3 Details eIF-2-alpha kinase GCN2 Q9P2K8 Details Ephrin type-A receptor 6 Q9UF33 Details Leucine-rich repeat serine/threonine-protein kinase 2 Q5S007 Details Mitogen-activated protein kinase kinase kinase 3 Q99759 Details Mitogen-activated protein kinase kinase kinase kinase 4 O95819 Details MAP kinase-activated protein kinase 5 Q8IW41 Details CLIP-associating protein 1 Q7Z460 Details Megakaryocyte-associated tyrosine-protein kinase P42679 Details Serine/threonine-protein kinase Nek1 Q96PY6 Details Serine/threonine-protein kinase PAK 4 O96013 Details Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase Q99640 Details Serine/threonine-protein kinase RIO1 Q9BRS2 Details SNF-related serine/threonine-protein kinase Q9NRH2 Details Serine/threonine-protein kinase 10 O94804 Details Exportin-1 O14980 Details Mitogen-activated protein kinase 6 Q16659 Details Solute carrier family 43 member 3 Q8NBI5 Details Lysophosphatidic acid receptor 6 P43657 Details Solute carrier family 41 member 1 Q8IVJ1 Details Y+L amino acid transporter 2 Q92536 Details Receptor for retinol uptake STRA6 Q9BX79 Details Zinc transporter ZIP10 Q9ULF5 Details Zinc transporter 7 Q8NEW0 Details Zinc transporter 8 Q8IWU4 Details Zinc transporter 5 Q8TAD4 Details Zinc transporter 10 Q6XR72 Details Zinc transporter ZIP13 Q96H72 Details Zinc transporter 6 Q6NXT4 Details Diacylglycerol kinase eta Q86XP1 Details V-type proton ATPase subunit e 2 Q8NHE4 Details V-type proton ATPase 116 kDa subunit a isoform 1 Q93050 Details Plasma membrane calcium-transporting ATPase 4 P23634 Details Calcium-transporting ATPase type 2C member 2 O75185 Details PI-PLC X domain-containing protein 3 Q63HM9 Details Lysine-specific histone demethylase 1A O60341 Details Signal transducer and activator of transcription 1-alpha/beta P42224 Details Nuclear factor erythroid 2-related factor 2 Q16236 Details 3-oxoacyl-[acyl-carrier-protein] reductase Q8N4T8 Details IgG receptor FcRn large subunit p51 P55899 Details