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(12) United States Patent (10) Patent No.: US 6,989,232 B2 Burgess Et Al

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(12) United States Patent (10) Patent No.: US 6,989,232 B2 Burgess Et Al USOO6989232B2 (12) United States Patent (10) Patent No.: US 6,989,232 B2 Burgess et al. (45) Date of Patent: Jan. 24, 2006 (54) PROTEINS AND NUCLEIC ACIDS Adams et al, Nature 377 (Suppl), 3 (1995).* ENCODING SAME Nakayama et al, Genomics 51(1), 27(1998).* Mahairas et al. Accession No. B45150 (Oct. 21, 1997).* (75) Inventors: Catherine E. Burgess, Wethersfield, Wallace et al, Methods Enzymol. 152: 432 (1987).* CT (US); Pamela B. Conley, Palo Alto, GenBank Accession No.: CAB01233 (Jun. 20, 2001). CA (US); William M. Grosse, SWALL (SPTR) Accession No.: Q9N4G7 (Oct. 1, 2000). Branford, CT (US); Matthew Hart, San GenBank Accession No.: Z77666 (Jun. 20, 2001). Francisco, CA (US); Ramesh Kekuda, GenBank Accession No. XM 038002 (Oct. 16, 2001). Stamford, CT (US); Richard A. GenBank Accession No. XM 039746 (Oct. 16, 2001). Shimkets, West Haven, CT (US); GenBank Accession No.: AAF51854 (Oct. 4, 2000). Kimberly A. Spytek, New Haven, CT GenBank Accession No.: AAF52569 (Oct. 4, 2000). (US); Edward Szekeres, Jr., Branford, GenBank Accession No.: AAF53188 (Oct. 4, 2000). CT (US); James E. Tomlinson, GenBank Accession No.: AAF55 108 (Oct. 5, 2000). Burlingame, CA (US); James N. GenBank Accession No.: AAF58048 (Oct. 4, 2000). Topper, Los Altos, CA (US); Ruey-Bin GenBank Accession No.: AAF59281 (Oct. 4, 2000). Yang, San Mateo, CA (US) GenBank Accession No.: AE003598 (Oct. 4, 2000). GenBank Accession No.: AE003619 (Oct. 4, 2000). (73) Assignees: Millennium Pharmaceuticals, Inc., GenBank Accession No.: AE003636 (Oct. 4, 2000). Cambridge, MA (US); Curagen GenBank Accession No.: AE003706 (Oct. 5, 2000). Corporation, New Haven, CT (US) GenBank Accession No.: AE003808 (Oct. 4, 2000). GenBank Accession No.: AE003842 (Oct. 4, 2000). (*) Notice: Subject to any disclaimer, the term of this SWALL (SPTR) Accession No.: Q9V419 (May 1, 2000). patent is extended or adjusted under 35 SWALL (SPTR) Accession No.: Q9V7K1 (May 1, 2000). U.S.C. 154(b) by 339 days. SWALL (SPTR) Accession No.: Q9VFF2 (May 1, 2000). SWALL (SPTR) Accession No.: Q9VK90 (May 1, 2000). (21) Appl. No.: 09/939,853 SWALL (SPTR) Accession No.: Q9VLW2 (May 1, 2000). (22) Filed: Aug. 27, 2001 SWALL (SPTR) Accession No.: Q9VNR8 (May 1, 2000). GenBank Accession No.: U72744 (Feb. 1, 1997). (65) Prior Publication Data Alderborn, et al. (2000). “Determination of single-nucle US 2004/0039163 A1 Feb. 26, 2004 otide polymorphisms by real-time pyrophosphate DNA sequencing.” Genome Res. 10(8): 1249-1258. Related U.S. Application Data Alessi, et al. (1997). “3-Phosphoinositide-dependent pro (60) Provisional application No. 60/228,191, filed on Aug. 25, tein kinase-1 (PDK1): structural and functional homology 2000, provisional application No. 60/267,300, filed on Feb. 8, 2001, provisional application No. 60/269,961, filed on with the Drosophila DSTPK61 kinase.” Curr. Biol. 7(10): Feb. 20, 2001, and provisional application No. 60/277,337, 776-789. filed on Mar. 20, 2001. Alessi, et al. (1997). “Characterization of a 3-phosphoi nositide-dependent protein kinase which phosphorylates (51) Int. Cl. and activates protein kinase Balpha.” Curr. Biol. 7(4): CI2O I/68 (2006.01) 261-269. GenBank Accession No.: AAC50357 (Sep. 12, 2000). (52) U.S. Cl. ..................... 435/6; 435/252.3; 435/320.1; GenBank Accession No. U30473 (Sep. 12, 2000). 435/325; 435/252.33; 514/44; 536/23.1; SWALL (SPTR) Accession No.: Q13239 (Nov. 1, 1996). 536/23.5 GenBank Accession No.: AAC48618 (Aug. 22, 1996). (58) Field of Classification Search ................ 536/23.1, 536/23.5, 23.2; 514/44; 435/6, 320.1, 325, (Continued) 435/252.3, 252.33 See application file for complete Search history. Primary Examiner James Martinell (74) Attorney, Agent, O Firm-Millennium (56) References Cited Pharmaceuticals, Inc. U.S. PATENT DOCUMENTS (57) ABSTRACT 4,350,764 A * 9/1982 Baxter et al. .............. 435/69.4 Disclosed herein are nucleic acid Sequences that encode novel polypeptides. Also disclosed are polypeptides encoded FOREIGN PATENT DOCUMENTS by these nucleic acid Sequences, and antibodies, which EP 1033401 6/2000 immunospecifically-bind to the polypeptide, as well as EP 1033405 6/2000 derivatives, variants, mutants, or fragments of the aforemen EP 1074617 7/2001 tioned polypeptide, polynucleotide, or antibody. The inven WO WO OO/O9552 2/2000 tion further discloses therapeutic, diagnostic and research methods for diagnosis, treatment, and prevention of disor OTHER PUBLICATIONS derS involving any one of these novel human nucleic acids GenBank Accession No. AC026539 (Apr. 27, 2000).* and proteins. Pharmacia P-L Biochemicals 1984 Product Reference Guide (pp. 36–37).* 38 Claims, No Drawings US 6,989.232 B2 Page 2 OTHER PUBLICATIONS Hurd and Saxton (1996). “Kinesin mutations cause motor neuron disease phenotypes by disrupting fast axonal trans GenBank Accession No .: AAC50646 (Aug. 22, 1996). port in Drosophila.” Genetics 144(3): 1075–1085. GenBank Accession No .: U23028 (Aug. 22, 1996). SWALL (SPTR) Accession No.: Q9H875 (Mar. 1, 2000). GenBank Accession No .: AL035424 (Nov. 23, 1999). SWALL (SPTR) Accession No.: Q9H955 (Mar. 1, 2000). GenBank Accession No ..: CAB39994 (Nov. 23, 1999). GenBank Accession No.: AKO01921 (Feb. 22, 2000). SWALL (SPTR) Accession No.: Q9COH6 (Oct. 16, 2001). GenBank Accession No.: AK021895 (Sep. 29, 2000). SWALL (SPTR) Accession No.: Q9Y3J5 (Oct. 16, 2001). GenBank Accession No.: AK023057 (Sep. 29, 2000). Burn, et al. (1996). “Generation of a transcriptional map for GenBank Accession No.: AK023964 (Sep. 29, 2000). a 700-kb region Surrounding the polycystic kidney disease GenBank Accession No ... BAB14382 (Sep. 29, 2000). type 1 (PKD1) and tuberous sclerosis type 2 (TSC2) disease GenBank Accession No ... BAB14742 (Sep. 29, 2000). genes on human chromosome 16p3.3.” Genome Res. 6(6): SWALL (SPTR) Accession No.: Q55909 (Nov. 1, 1997). 525-537. GenBank Accession No .: BAA10672 (Jul. 4, 2001). GenBank Accession : AKO03661 (Jul. 5, 2001). GenBank Accession No .: AKO25645 (Sep. 29, 2000). GenBank Accession : AKO05100 (Jul. 5, 2001). GenBank Accession No ... BAB15201 (Sep. 29, 2000). GenBank Accession : AKO07036 (Jul. 5, 2001). SWALL (SPTR) Accession No.: Q9H6O3 (May 1, 2001). GenBank Accession .: AKO10359 (Jul. 5, 2001). SWALL (SPTR) Accession No.: Q9CQZ1 (Jun. 1, 2001). GenBank Accession : AKO18438 (Jul. 5, 2001). SWALL (SPTR) Accession No.: Q9CVQ1 (Jun. 1, 2001). GenBank Accession : AKO18708 (Jul. 5, 2001). SWALL (SPTR) Accession No.: Q9CW36 (Jun. 1, 2001). GenBank Accession : AKO20837 (Jul. 5, 2001). SWALL (SPTR) Accession No.: Q9CWV6 (Jun. 1, 2001). GenBank Accession : BAB22923 (Jul. 5, 2001). SWALL (SPTR) Accession No.: Q9CXA5 (Jun. 1, 2001). GenBank Accession : BAB23818 (Jul. 5, 2001). SWALL (SPTR) Accession No.: Q9CY32 (Jun. 1, 2001). GenBank Accession ... BAB24835 (Jul. 5, 2001). SWALL (SPTR) Accession No.: Q9D1E2 (Jun. 1, 2001). GenBank Accession : BAB26879 (Jul. 5, 2001). SWALL (SPTR) Accession No. : Q9D1Z9 (Jun. 1, 2001). GenBank Accession : BAB31212 (Jul. 5, 2001). GenBank Accession No .: O15438 (Aug. 20, 2001). GenBank Accession : BAB31359 (Jul. 5, 2001). GenBank Accession N .: BAA28146 (Feb. 13, 1999). GenBank Accession ... BAB32223 (Jul. 5, 2001). GenBank Accession N .: AAA36741 (Sep. 15, 1994). SWALL (SPTR) Acc C ssion No.: Q9SN75 (May 1, 2000). GenBank Accession N : M25631 (Sep. 15, 1994). GenBank Accession OO : AL132955 (Nov. 30, 1999). GenBank Accession N : CAA76658 (May 12, 1999). GenBank Accession ..: CAB61989 (Nov. 30, 1999). GenBank Accession N : AAD01430 (Jun. 22, 1999). GenBank Accession ... AAB46616 (Feb. 10, 1997). GenBank Accession N : AAA61178 (Jan. 14, 1995). GenBank Accession : P33527 (Mar. 1, 2001). GenBank Accession N ..: CAA28370 (Mar 21, 1995). GenBank Accession : D64005 (Oct. 8, 1999). GenBank Accession N : P07996 (Aug. 20, 2001). GenBank Accession : AAB17690 (Oct. 30, 1996). GenBank Accession N : AAF02111 (Jan. 24, 2001). GenBank Accession : U19516 (Oct. 30, 1996). GenBank Accession N : AC009755 (Jan. 24, 2001). GenBank Accession GenBank Accession N : AAC12836 (Apr. 5, 2000). : AAB83979 (Nov. 6, 1997). GenBank Accession No : AC004238 (Apr. 5, 2000). GenBank Accession No.: AAB83983 (Nov. 6, 1997). SWALL (SPTR) Accession No.: O64760 (Aug. 1, 1998). GenBank Accession No.:O AF022853 (Nov. 8, 1997). SWALL (SPTR) Accession No.: Q9SRU3 (May 1, 2001). SWALL (SPTR) Accession No.: Q9UQ99 (May 1, 2000). GenBank Accession No .: AL050318 (Jul. 20, 2001). GenBank Accession No.: AJ251892 (Dec. 22, 1999). GenBank Accession No ..: CAB75365 (Jul. 20, 2001). GenBank Accession No.: CAB64381 (Dec. 22, 1999). SWALL (SPTR) Accession No.: Q9H135 (May 1, 2001). SWALL (SPTR) Accession No.: Q9U111 (May 1, 2000). GenBank Accession No ... AAC27662 (Jul. 28, 1998). Gubb and Garcia-Bellido (1982). “A genetic analysis of the GenBank Accession No .: AB054031 (Jul 27, 2001). determination of cuticular polarity during development in GenBank Accession No ... BAB32487 (Jul 27, 2001). Drosophila melanogaster.” J. Embryol. Exp. Morphol. 68: SWALL (SPTR) Accession No.: Q99PT4 (Jun. 1, 2001). 37-57. SWALL (SPTR) Accession No.: Q99PU2 (Jun. 1, 2001). GenBank Accession No.: AAD55929 (Sep. 21, 1999). 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